scholarly journals Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

2020 ◽  
Author(s):  
Danny Ionescu ◽  
Luca Zoccarato ◽  
Artur Zaduryan ◽  
Sina Schorn ◽  
Mina Bizic ◽  
...  
Keyword(s):  
Species Concept ◽  
Single Cells ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Allelic Diversity ◽  
Evolutionary Mechanisms ◽  
Genomic Features ◽  
Bacterial Speciation ◽  
Depth Ranges ◽  
Functional Versatility

Abstract Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

scholarly journals Heterozygous, polyploid, giant bacterium, Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

2020 ◽  
Author(s):  
Danny Ionescu ◽  
Luca Zoccarato ◽  
Artur Zaduryan ◽  
Sina Schorn ◽  
Mina Bižić ◽  
...  
Keyword(s):  
Species Concept ◽  
Phylogenetic Signal ◽  
Single Cells ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Allelic Diversity ◽  
Evolutionary Mechanisms ◽  
Bacterial Speciation ◽  
Depth Ranges ◽  
Functional Versatility

AbstractAchromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we show Achromatia are common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless, Achromatia display no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory. Achromatia cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

scholarly journals The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms

Micromachines ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 367 ◽  
Author(s):  
Yuguang Liu ◽  
Dirk Schulze-Makuch ◽  
Jean-Pierre de Vera ◽  
Charles Cockell ◽  
Thomas Leya ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Bacterial Species ◽  
Cell Manipulation ◽  
Microfluidic Platforms ◽  
Gram Positive ◽  
Gram Negative ◽  
Genome Amplification ◽  
Single Cell Sequencing ◽  
Wide Range

Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.

scholarly journals A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma

2022 ◽  
Vol 14 (1) ◽  
Author(s):  
Thinh T. Nguyen ◽  
Hyun-Sung Lee ◽  
Bryan M. Burt ◽  
Jia Wu ◽  
Jianjun Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Lung Adenocarcinoma ◽  
Gene Expression Analysis ◽  
Immune Cell ◽  
Expression Patterns ◽  
Immune Cell Infiltration ◽  
Histological Subtypes ◽  
Genomic Features ◽  
Differential Gene

Abstract Background Lung adenocarcinoma, the most common type of lung cancer, has a high level of morphologic heterogeneity and is composed of tumor cells of multiple histological subtypes. It has been reported that immune cell infiltration significantly impacts clinical outcomes of patients with lung adenocarcinoma. However, it is unclear whether histologic subtyping can reflect the tumor immune microenvironment, and whether histologic subtyping can be applied for therapeutic stratification of the current standard of care. Methods We inferred immune cell infiltration levels using a histological subtype-specific gene expression dataset. From differential gene expression analysis between different histological subtypes, we developed two gene signatures to computationally determine the relative abundance of lepidic and solid components (denoted as the L-score and S-score, respectively) in lung adenocarcinoma samples. These signatures enabled us to investigate the relationship between histological composition and clinical outcomes in lung adenocarcinoma using previously published datasets. Results We found dramatic immunological differences among histological subtypes. Differential gene expression analysis showed that the lepidic and solid subtypes could be differentiated based on their gene expression patterns while the other subtypes shared similar gene expression patterns. Our results indicated that higher L-scores were associated with prolonged survival, and higher S-scores were associated with shortened survival. L-scores and S-scores were also correlated with global genomic features such as tumor mutation burdens and driver genomic events. Interestingly, we observed significantly decreased L-scores and increased S-scores in lung adenocarcinoma samples with EGFR gene amplification but not in samples with EGFR gene mutations. In lung cancer cell lines, we observed significant correlations between L-scores and cell sensitivity to a number of targeted drugs including EGFR inhibitors. Moreover, lung cancer patients with higher L-scores were more likely to benefit from immune checkpoint blockade therapy. Conclusions Our findings provided further insights into evaluating histology composition in lung adenocarcinoma. The established signatures reflected that lepidic and solid subtypes in lung adenocarcinoma would be associated with prognosis, genomic features, and responses to targeted therapy and immunotherapy. The signatures therefore suggested potential clinical translation in predicting patient survival and treatment responses. In addition, our framework can be applied to other types of cancer with heterogeneous histological subtypes.

scholarly journals ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes

2020 ◽  
Author(s):  
Kenneth H. Hu ◽  
John P. Eichorst ◽  
Chris S. McGinnis ◽  
David M. Patterson ◽  
Eric D. Chow ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Real Time ◽  
Dimensional Space ◽  
Single Cells ◽  
Expression Patterns ◽  
Live Cells ◽  
Glass Substrates ◽  
Complete Mapping

ABSTRACTSpatial transcriptomics seeks to integrate single-cell transcriptomic data within the 3-dimensional space of multicellular biology. Current methods use glass substrates pre-seeded with matrices of barcodes or fluorescence hybridization of a limited number of probes. We developed an alternative approach, called ‘ZipSeq’, that uses patterned illumination and photocaged oligonucleotides to serially print barcodes (Zipcodes) onto live cells within intact tissues, in real-time and with on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in-vitro wound healing, live lymph node sections and in a live tumor microenvironment (TME). In all cases, we discovered new gene expression patterns associated with histological structures. In the TME, this demonstrated a trajectory of myeloid and T cell differentiation, from periphery inward. A variation of ZipSeq efficiently scales to the level of single cells, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.

scholarly journals Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Marcel Tarbier ◽  
Sebastian D. Mackowiak ◽  
João Frade ◽  
Silvina Catuara-Solarz ◽  
Inna Biryukova ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Nuclear Organization ◽  
Single Cells ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Nuclear Gene ◽  
Biological Properties ◽  
Sequencing Studies ◽  
Genes Encoding ◽  
Functional Regulation

Abstract Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.

scholarly journals Expression Profiling of Single Mammalian Cells – Small is Beautiful

Yeast ◽  
2000 ◽  
Vol 1 (3) ◽  
pp. 211-217 ◽  
Author(s):  
Gerard Brady
Keyword(s):  
Mrna Expression ◽  
Single Cell ◽  
Mammalian Cells ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Small Samples ◽  
Biological Research ◽  
Cell Expression

Increasingly mRNA expression patterns established using a variety of molecular technologies such as cDNA microarrays, SAGE and cDNA display are being used to identify potential regulatory genes and as a means of providing valuable insights into the biological status of the starting sample. Until recently, the application of these techniques has been limited to mRNA isolated from millions or, at very best, several thousand cells thereby restricting the study of small samples and complex tissues. To overcome this limitation a variety of amplification approaches have been developed which are capable of broadly evaluating mRNA expression patterns in single cells. This review will describe approaches that have been employed to examine global gene expression patterns either in small numbers of cells or, wherever possible, in actual isolated single cells. The first half of the review will summarize the technical aspects of methods developed for single-cell analysis and the latter half of the review will describe the areas of biological research that have benefited from single-cell expression analysis.

scholarly journals Emergent multicellular life cycles in filamentous bacteria owing to density-dependent population dynamics

2011 ◽  
Vol 8 (65) ◽  
pp. 1772-1784 ◽  
Author(s):  
Valentina Rossetti ◽  
Manuela Filippini ◽  
Miroslav Svercel ◽  
A. D. Barbour ◽  
Homayoun C. Bagheri
Keyword(s):  
Cell Division ◽  
Population Growth ◽  
Generation Time ◽  
Single Cells ◽  
Bacterial Species ◽  
Life Forms ◽  
Life Cycles ◽  
Morphological Properties ◽  
Filamentous Bacteria ◽  
Growth Phases

Filamentous bacteria are the oldest and simplest known multicellular life forms. By using computer simulations and experiments that address cell division in a filamentous context, we investigate some of the ecological factors that can lead to the emergence of a multicellular life cycle in filamentous life forms. The model predicts that if cell division and death rates are dependent on the density of cells in a population, a predictable cycle between short and long filament lengths is produced. During exponential growth, there will be a predominance of multicellular filaments, while at carrying capacity, the population converges to a predominance of short filaments and single cells. Model predictions are experimentally tested and confirmed in cultures of heterotrophic and phototrophic bacterial species. Furthermore, by developing a formulation of generation time in bacterial populations, it is shown that changes in generation time can alter length distributions. The theory predicts that given the same population growth curve and fitness, species with longer generation times have longer filaments during comparable population growth phases. Characterization of the environmental dependence of morphological properties such as length, and the number of cells per filament, helps in understanding the pre-existing conditions for the evolution of developmental cycles in simple multicellular organisms. Moreover, the theoretical prediction that strains with the same fitness can exhibit different lengths at comparable growth phases has important implications. It demonstrates that differences in fitness attributed to morphology are not the sole explanation for the evolution of life cycles dominated by multicellularity.

scholarly journals High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

2020 ◽  
Author(s):  
Wenjing Tao ◽  
Luohao Xu ◽  
Lin Zhao ◽  
Zexian Zhu ◽  
Xin Wu ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Nile Tilapia ◽  
Sex Chromosome ◽  
Expression Patterns ◽  
Heterochromatic Region ◽  
Single Nucleotide Variants ◽  
Evolutionary Mechanisms ◽  
Unequal Distribution ◽  
Functional Studies ◽  
Blue Tilapia

AbstractBackgroundTilapias are one of the most farmed fishes that are coined as ‘aquatic chicken’ by the food industry. Like many other teleosts, Nile tilapia and blue tilapia exhibit very recent transition of sex chromosome systems since their divergence about 5 million years ago, making them a great model for elucidating the molecular and evolutionary mechanisms of sex chromosome turnovers. Studies into their sex-determining pathways are also critical for developing genetic sex control in aquaculture.ResultsWe report here the newly produced genomes of Nile tilapia and blue tilapia that integrate long-read sequencing and chromatin conformation data. The two nearly complete genomes have anchored over 97% of the sequences into linkage groups (LGs), and assembled majorities of complex repetitive regions including telomeres, centromeres and rDNA clusters. In particular, we inferred two episodes of repeat expansion at LG3 respectively in the ancestor of cichlids and that of tilapias. The consequential large heterochromatic region concentrated at one end of LG3 comprises tandem arrays of mRNA and small RNA genes, among which we have identified a candidate female determining gene Paics in blue tilapia. Paics show female-specific patterns of single-nucleotide variants, copy numbers and expression patterns in gonads during early gonadogenesis.ConclusionsOur work provide a very important genomic resource for functional studies of cichlids, and suggested that unequal distribution of repeat content that impacts the local recombination rate might make some chromosomes more likely to become sex chromosomes.

scholarly journals AmpC β-Lactamase Variable Expression in Common Multidrug-Resistant Nosocomial Bacterial Pathogens from a Tertiary Hospital in Cairo, Egypt

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Aliaa ELshamy ◽  
Zainab Zakaria ◽  
Mahmoud M. Tolba ◽  
Nermeen Salah Eldin ◽  
Al-Taher Rabea ◽  
...  
Keyword(s):  
Tract Infection ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Tertiary Hospital ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Variable Expression ◽  
Wound Swab ◽  
Significant Difference ◽  
Lactamase Gene

The emergence of AmpC (pAmpC) β-lactamases conferring resistance to the third-generation cephalosporins has become a major clinical concern worldwide. In this study, we aimed to evaluate the expression of AmpC β-lactamase encoding gene among the pathogenic Gram-positive and Gram-negative resistant bacteria screened from clinical samples of Egyptian patients enrolled into El-Qasr El-Ainy Tertiary Hospital in Cairo, Egypt. A total of 153 bacterial isolates of the species Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecium were isolated from patients diagnosed with urinary tract infection (UTI), respiratory tract infection (RTI), and wound infections. The total number of E. faecium isolates was 53, comprising 29 urine isolates, 5 sputum isolates, and 19 wound swab isolates, whereas the total number of P. aeruginosa isolates was 49, comprising 27 urine isolates, 7 sputum isolates, and 15 wound swab isolates, and that of the K. pneumoniae isolates was 51, comprising 20 urine isolates, 25 sputum isolates, and 6 wound swab isolates. Our results indicated that there is no significant difference in the expression of AmpC β-lactamase gene among the tested bacterial species with respect to the type of infection and/or clinical specimen. However, the expression patterns of AmpC β-lactamase gene markedly differed according to the antibacterial resistance characteristics of the tested isolates.

scholarly journals A network regularized linear model to infer spatial expression pattern for single cells

2021 ◽  
Author(s):  
Chaohao Gu ◽  
Zhandong Liu
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Spatial Information ◽  
Expression Profiles ◽  
Single Cells ◽  
Expression Patterns ◽  
Capture Rate ◽  
Marker Genes ◽  
Spatial Expression ◽  
Cellular Expression

Abstract Spatial gene-expression is a crucial determinant of cell fate and behavior. Recent imaging and sequencing-technology advancements have enabled scientists to develop new tools that use spatial information to measure gene-expression at close to single-cell levels. Yet, while Fluorescence In-situ Hybridization (FISH) can quantify transcript numbers at single-cell resolution, it is limited to a small number of genes. Similarly, slide-seq was designed to measure spatial-expression profiles at the single-cell level but has a relatively low gene-capture rate. And although single-cell RNA-seq enables deep cellular gene-expression profiling, it loses spatial information during sample-collection. These major limitations have stymied these methods’ broader application in the field. To overcome spatio-omics technology’s limitations and better understand spatial patterns at single-cell resolution, we designed a computation algorithm that uses glmSMA to predict cell locations by integrating scRNA-seq data with a spatial-omics reference atlas. We treated cell-mapping as a convex optimization problem by minimizing the differences between cellular-expression profiles and location-expression profiles with an L1 regularization and graph Laplacian based L2 regularization to ensure a sparse and smooth mapping. We validated the mapping results by reconstructing spatial- expression patterns of well-known marker genes in complex tissues, like the mouse cerebellum and hippocampus. We used the biological literature to verify that the reconstructed patterns can recapitulate cell-type and anatomy structures. Our work thus far shows that, together, we can use glmSMA to accurately assign single cells to their original reference-atlas locations.

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