Read by QxMD icon Read

Cell lineage tree

Nickias Kienle, Tobias H Kloepper, Dirk Fasshauer
BACKGROUND: A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization...
October 18, 2016: BMC Evolutionary Biology
Chaim A Schramm, Zizhang Sheng, Zhenhai Zhang, John R Mascola, Peter D Kwong, Lawrence Shapiro
The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest...
2016: Frontiers in Immunology
Sook-Kyung Lee, Shuntai Zhou, Pedro L Baldoni, Ean Spielvogel, Nancie M Archin, Michael G Hudgens, David M Margolis, Ronald Swanstrom
BACKGROUND: In this study, we measured the latent HIV-1 reservoir harboring replication-competent HIV-1 in resting CD4+ T cells in participants on highly active antiretroviral therapy (HAART), quantitating the frequency of latent infection through the use of a Primer ID-based Ultra Deep Sequencing Assay (UDSA), in comparison to the readout of the quantitative viral outgrowth assay (QVOA). METHODS: Viral RNA derived from culture wells of QVOA that scored as HIV-1 p24 capsid (CA) antigen-positive were tagged with a specific barcode during cDNA synthesis, and the sequences within the V1-V3 region of the HIV-1 env gene were analyzed for diversity using the Primer ID-based paired-end MiSeq platform...
September 27, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
Josef C Uyeda, Luke J Harmon, Carrine E Blank
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria...
2016: PloS One
Fabrícia F Nascimento, Allen G Rodrigo
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy...
2016: PloS One
Thijmen Breeschoten, Camiel Doorenweerd, Sergei Tarasov, Alfried P Vogler
Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini...
December 2016: Molecular Phylogenetics and Evolution
Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M Barr, Ruth Halaban, Ehud Shapiro
Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single cell sequencing, which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data and uses it to generate a lineage tree of the input cells...
August 24, 2016: Genome Research
Chao-Kai Kang, Chia-Shian Lin, Yao-Chung Hu, Shu-Chuan Tsai, Tsung-Han Lee
Milkfish, a species within the primitive teleost lineage Otocephala, can survive in water conditions ranging from hypo- to hyper-saline. This study explored the effects of environmental salinity on apical morphologies of ionocytes and the expression of villin homologs in the gills of milkfish acclimated to either seawater (SW) or fresh water (FW). Scanning electron microscopy revealed that the ionocytes in the gill filaments of SW and FW milkfish, respectively, cellular apical morphologies were hole-type and squint-type...
August 21, 2016: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
Bradly Alicea, Richard Gordon
Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa...
2016: Biology
Yosuke Sakai, Ariko Miyake, Naoya Doi, Hikari Sasada, Yasuyuki Miyazaki, Akio Adachi, Masako Nomaguchi
Viruses of human immunodeficiency virus type 2 (HIV-2) and some simian immunodeficiency virus (SIV) lineages carry a unique accessory protein called Vpx. Vpx is essential or critical for viral replication in natural target cells such as macrophages and T lymphocytes. We have previously shown that a poly-proline motif (PPM) located at the C-terminal region of Vpx is required for its efficient expression in two strains of HIV-2 and SIVmac, and that the Vpx expression levels of the two clones are significantly different...
2016: Frontiers in Microbiology
Vladimir V Aleoshin, Alexander P Mylnikov, Gulnara S Mirzaeva, Kirill V Mikhailov, Sergey A Karpov
Heterotrophic lineages of Heterokonta (or stramenopiles), in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heterotrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor...
2016: Frontiers in Microbiology
Dae In Kim, Ji Hee Lee, Joo Won Kang, Jong-Ok Ka, Chi Nam Seong
A motile and rod-shaped bacterium, designated strain KYW1030T, was isolated from seawater collected from the Gwangyang bay (Republic of Korea). Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were summed feature 4 (C17:1 iso I and/or anteiso B), iso-C15:0, iso-C17:0 3-OH. The strain contained MK-7 as the major isoprenoid quinone, phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids and sym-homospermidine as the major polyamine...
August 4, 2016: International Journal of Systematic and Evolutionary Microbiology
Ji Hee Lee, Mi Sun Kim, Joo Won Kang, Keun Sik Baik, Chi Nam Seong
A non-motile, rod-shaped and pale-pink colored bacterium, designated strain WS71T, was isolated from freshwater collected from the Woopo Wetland (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- positive and oxidase- negative. The major fatty acids were summed feature 3 (comprising C16:1 6c and/or C16:1 7c), iso-C17:0 3-OH, C16:0 and iso-C15:0. The strain contained menaquinone 7 (MK-7) and the DNA G+C content was 39.4±0.4 mol%. The major polar lipids were phosphatidylethanolamine and unknown amino lipid...
August 5, 2016: International Journal of Systematic and Evolutionary Microbiology
Rebecca Rose, Susanna L Lamers, David J Nolan, Ekaterina Maidji, N R Faria, Oliver G Pybus, James J Dollar, Samuel A Maruniak, Andrew C McAvoy, Marco Salemi, Cheryl A Stoddart, Elyse J Singer, Michael S McGrath
UNLABELLED: While combined antiretroviral therapy (cART) can result in undetectable plasma viral loads, it does not eradicate HIV infection. Furthermore, HIV-infected individuals while on cART remain at an increased risk of developing serious comorbidities, such as cancer, neurological disease, and atherosclerosis, suggesting that during cART, tissue-based HIV may contribute to such pathologies. We obtained DNA and RNA env, nef, and pol sequences using single-genome sequencing from postmortem tissues of three HIV(+) cART-treated (cART(+)) individuals with undetectable viral load and metastatic cancer at death and performed time-scaled Bayesian evolutionary analyses...
October 15, 2016: Journal of Virology
Man Cao, Yuwei Chenzhang, Xianping Ding, Yiwen Zhang, Yaling Jing, Zuyi Chen
Human papillomaviruses (HPVs) are circular double-stranded DNA viruses that are highly prevalent in the general population, and account for the cervical cancer burden in women worldwide. In this study, we analyzed HPV-16, the most prevalent type worldwide, and HPV-53, a possible high-risk type from infected women in Southwest China. To characterize mutations, intratypic variants, and genetic variability in the E6, E7, and L1 genes of HPV-16 (n=97) and HPV-53 (n=15), these genes were sequenced and submitted to GenBank...
October 30, 2016: Gene
Mark Q Martindale
Ctenophores are a clade of animals that branch off at the base of the animal tree. They have a unique and delicate body plan, and distinct pattern forming mechanisms at different life history stages. They have a stereotyped embryonic cell lineage and are highly 'mosaic' as embryos, but most have amazing capacity to regenerate as adults. Unfortunately, only a handful of ctenophore species have been studied in detail. This review summarizes the key features of the regenerative properties of adults, and the characteristics of the embryological onset of regenerative abilities...
July 12, 2016: Current Opinion in Genetics & Development
Surintorn Boonanuntanasarn, Paiboon Bunlipatanon, Kensuke Ichida, Kirana Yoohat, Ornkanya Mengyu, Samart Detsathit, Ryosuke Yazawa, Goro Yoshizaki
The vasa gene is specifically expressed in the germ cell lineage, and its expression has been used to study germline development in many organisms, including fishes. In this study, we cloned and characterized vasa as Efu-vasa in the brown-marbled grouper (Epinephelus fuscoguttatus). Efu-vasa contained predicted regions that shared consensus motifs with the vasa family in teleosts, including arginine- and glycine-rich repeats, ATPase motifs, and a DEAD box. Phylogenetic-tree construction using various DEAD-box proteins confirmed that Efu-vasa was clustered in the vasa family...
July 12, 2016: Fish Physiology and Biochemistry
Leïla Perié, Ken R Duffy
The dynamic process by which self-renewing stem cells and their offspring proliferate and differentiate to create the erythroid, myeloid and lymphoid lineages of the blood system has long since been an important topic of study. A range of recent single cell and family-tracing methodologies such as massively parallel single-cell RNA-sequencing, mass cytometry, integration site barcoding, cellular barcoding and transposon barcoding are enabling unprecedented analysis, dissection and re-evaluation of the hematopoietic tree...
July 12, 2016: FEBS Letters
Dongyan Wang, Yi Xu, Yong Zhang, Shuangli Zhu, Yuan Si, Dongmei Yan, Hui Zhu, Qian Yang, Tianjiao Ji, Wenbo Xu
We analyzed the genetic characteristics of coxsackievirus A4 (CV-A4) based on the entire VP1 coding region. Samples were isolated from patients with acute flaccid paralysis (AFP) in Shaanxi, China from 2006 to 2010. We wished to ascertain the predominant genotype and the relationship between CV-A4 infection and AFP. Sixty-eight non-polio enteroviruses were inoculated onto RD cells (to increase the virus titer) and molecular typing was undertaken. The entire VP1 coding region was amplified. Percentage of CV-A4 was 10...
March 2016: Bing du Xue Bao, Chinese Journal of Virology
Miho Kobayashi, Yuki Matsushima, Takumi Motoya, Naomi Sakon, Naoki Shigemoto, Reiko Okamoto-Nakagawa, Koichi Nishimura, Yasutaka Yamashita, Makoto Kuroda, Nobuhiro Saruki, Akihide Ryo, Takeshi Saraya, Yukio Morita, Komei Shirabe, Mariko Ishikawa, Tomoko Takahashi, Hiroto Shinomiya, Nobuhiko Okabe, Koo Nagasawa, Yoshiyuki Suzuki, Kazuhiko Katayama, Hirokazu Kimura
Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10(-3) substitutions/site/year), resulting in three lineages...
2016: Scientific Reports
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"