scholarly journals Centromere size scales with genome size across Eukaryotes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Klára Plačková ◽  
Petr Bureš ◽  
František Zedek
Keyword(s):  
Genome Size ◽  
Positive Relationship ◽  
Strong Predictor ◽  
Methodological Approach ◽  
Grass Species ◽  
Common Mechanism ◽  
Phylogenetic Relatedness ◽  
Binding Domains ◽  
A Cell ◽  
Size Scales

AbstractPrevious studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. However, it is unclear whether this relationship is universal. Here we analyze the total centromere size using the CenH3-immunofluorescence area as a proxy in 130 taxa including plants, animals, fungi, and protists. We verified the reliability of our methodological approach by comparing our measurements with available ChIP-seq-based measurements of the size of CenH3-binding domains. Data based on these two independent methods showed the same positive relationship between the total centromere size and genome size. Our results demonstrate that the genome size is a strong predictor (R-squared = 0.964) of the total centromere size universally across Eukaryotes. We also show that this relationship is independent of phylogenetic relatedness and centromere type (monocentric, metapolycentric, and holocentric), implying a common mechanism maintaining stable total centromere size in Eukaryotes.

scholarly journals Centromere Size Scales With Genome Size Across Eukaryotes

2021 ◽  
Author(s):  
Klára Plačková ◽  
Petr Bureš ◽  
František Zedek
Keyword(s):  
Genome Size ◽  
Positive Relationship ◽  
Strong Predictor ◽  
Methodological Approach ◽  
Grass Species ◽  
Common Mechanism ◽  
Phylogenetic Relatedness ◽  
Binding Domains ◽  
A Cell ◽  
Size Scales

Abstract Previous studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. Here we analyze the total centromere size using the CenH3-immunofluorescence area as a proxy in 130 taxa including plants, animals, fungi, and protists. We verified the reliability of our methodological approach by comparing our measurements with available ChIP-seq-based measurements of the size of CenH3-binding domains. Data based on these two independent methods showed the same positive relationship between the total centromere size and genome size. Our results demonstrate that the genome size is a strong predictor (R-squared = 0.964) of the total centromere size universally across Eukaryotes. We also show that this relationship is independent of phylogenetic relatedness and centromere type (monocentric, metapolycentric, and holocentric), implying a common mechanism maintaining stable total centromere size in Eukaryotes.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

First estimates of genome size in ribbon worms (phylum Nemertea) using flow cytometry and Feulgen image analysis densitometry

2014 ◽  
Vol 92 (10) ◽  
pp. 847-851 ◽  
Author(s):  
Kelly L. Mulligan ◽  
Terra C. Hiebert ◽  
Nicholas W. Jeffery ◽  
T. Ryan Gregory
Keyword(s):  
Flow Cytometry ◽  
Image Analysis ◽  
Body Size ◽  
Genome Size ◽  
Positive Relationship ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Size Estimation ◽  
Size Diversity ◽  
Size Estimates

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indication of a positive relationship with body size. Somatic endopolyploidy also appears to be common in these animals. Importantly, this study demonstrates that both of the most common methods of genome-size estimation (flow cytometry and Feulgen image analysis densitometry) can be used to assess genome size in ribbon worms, thereby facilitating additional efforts to investigate patterns of variability in nuclear DNA content in this phylum.

scholarly journals The type II and X cellulose-binding domains of Pseudomonas xylanase A potentiate catalytic activity against complex substrates by a common mechanism

1999 ◽  
Vol 342 (2) ◽  
pp. 473-480 ◽  
Author(s):  
Jaitinder GILL ◽  
Jane E. RIXON ◽  
David N. BOLAM ◽  
Simon MCQUEEN-MASON ◽  
Peter J. SIMPSON ◽  
...  
Keyword(s):  
Microcrystalline Cellulose ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Wall Material ◽  
Common Mechanism ◽  
Type Ii ◽  
Binding Domains ◽  
Covalently Linked ◽  
Cellulose Binding ◽  
Internal Domain

Xylanase A (Pf Xyn10A), in common with several other Pseudomonas fluorescens subsp. cellulosa polysaccharidases, consists of a Type II cellulose-binding domain (CBD), a catalytic domain (Pf Xyn10ACD) and an internal domain that exhibits homology to Type X CBDs. The Type X CBD of Pf Xyn10A, expressed as a discrete entity (CBDX) or fused to the catalytic domain (Pf Xyn10A′), bound to amorphous and bacterial microcrystalline cellulose with a Ka of 2.5×105 M-1. CBDX exhibited no affinity for soluble forms of cellulose or cello-oligosaccharides, suggesting that the domain interacts with multiple cellulose chains in the insoluble forms of the polysaccharide. Pf Xyn10A′ was 2-3 times more active against cellulose-hemicellulose complexes than Pf Xyn10ACD; however, Pf Xyn10A′ and Pf Xyn10ACD exhibited the same activity against soluble substrates. CBDX did not disrupt the structure of plant-cell-wall material or bacterial microcrystalline cellulose, and did not potentiate Pf Xyn10ACD when not covalently linked to the enzyme. There was no substantial difference in the affinity of full-length Pf Xyn10A and the enzyme's Type II CBD for cellulose. The activity of Pf Xyn10A against cellulose-hemicellulose complexes was similar to that of Pf Xyn10A′, and a derivative of Pf Xyn10A in which the Type II CBD is linked to the Pf Xyn10ACD via a serine-rich linker sequence [Bolam, Cireula, McQueen-Mason, Simpson, Williamson, Rixon, Boraston, Hazlewood and Gilbert (1998) Biochem J. 331, 775-781]. These data indicate that CBDX is functional in Pf Xyn10A and that no synergy, either in ligand binding or in the potentiation of catalysis, is evident between the Type II and X CBDs of the xylanase.

scholarly journals HOTAIR, a cell cycle–associated long noncoding RNA and a strong predictor of survival, is preferentially expressed in classical and mesenchymal glioma

2013 ◽  
Vol 15 (12) ◽  
pp. 1595-1603 ◽  
Author(s):  
Jun-Xia Zhang ◽  
Lei Han ◽  
Zhao-Shi Bao ◽  
Ying-Yi Wang ◽  
Lu-Yue Chen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Strong Predictor ◽  
A Cell

scholarly journals Genome size is a strong predictor of cell size and stomatal density in angiosperms

2008 ◽  
Vol 179 (4) ◽  
pp. 975-986 ◽  
Author(s):  
Jeremy M. Beaulieu ◽  
Ilia J. Leitch ◽  
Sunil Patel ◽  
Arjun Pendharkar ◽  
Charles A. Knight
Keyword(s):  
Genome Size ◽  
Cell Size ◽  
Stomatal Density ◽  
Strong Predictor

ApuA, a multifunctional α-glucan-degrading enzyme of Streptococcus suis, mediates adhesion to porcine epithelium and mucus

Microbiology ◽  
2010 ◽  
Vol 156 (9) ◽  
pp. 2818-2828 ◽  
Author(s):  
Maria Laura Ferrando ◽  
Susana Fuentes ◽  
Astrid de Greeff ◽  
Hilde Smith ◽  
Jerry M. Wells
Keyword(s):  
Signal Sequence ◽  
Surface Protein ◽  
Normal Growth ◽  
Streptococcus Suis ◽  
Carbohydrate Utilization ◽  
Binding Domains ◽  
A Cell ◽  
Anchoring Motif

We have identified apuA in Streptococcus suis, which encodes a bifunctional amylopullulanase with conserved α-amylase and pullulanase substrate-binding domains and catalytic motifs. ApuA exhibited properties typical of a Gram-positive surface protein, with a putative signal sequence and LPKTGE cell-wall-anchoring motif. A recombinant protein containing the predicted N-terminal α-amylase domain of ApuA was shown to have α-(1,4) glycosidic activity. Additionally, an apuA mutant of S. suis lacked the pullulanase α-(1,6) glycosidic activity detected in a cell-surface protein extract of wild-type S. suis. ApuA was required for normal growth in complex medium containing pullulan as the major carbon source, suggesting that this enzyme plays a role in nutrient acquisition in vivo via the degradation of glycogen and food-derived starch in the nasopharyngeal and oral cavities. ApuA was shown to promote adhesion to porcine epithelium and mucus in vitro, highlighting a link between carbohydrate utilization and the ability of S. suis to colonize and infect the host.

scholarly journals Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer

2020 ◽  
Author(s):  
Sylvan C. Baca ◽  
David Y. Takeda ◽  
Ji-Heui Seo ◽  
Justin Hwang ◽  
Sheng Yu Ku ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Histone Modifications ◽  
Ectopic Expression ◽  
Resistance Mechanism ◽  
Regulatory Elements ◽  
Common Mechanism ◽  
Enhancer Activity ◽  
Adaptive Resistance ◽  
Neuroendocrine Prostate Cancer ◽  
A Cell

AbstractLineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer1,2. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. To investigate the epigenomic basis of this resistance mechanism, we profiled histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identified a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium3,4, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying novel cancer dependencies through epigenomic profiling.

scholarly journals Prolyl isomerase Pin1 and neurotrophins: a loop that may determine the fate of cells in cancer and neurodegeneration

2016 ◽  
Vol 9 (1) ◽  
pp. 59-62 ◽  
Author(s):  
Francesco Angelucci ◽  
Jakub Hort
Keyword(s):  
Signal Transduction ◽  
Conformational Changes ◽  
Neurodegenerative Disorders ◽  
Poor Prognosis ◽  
Suppressor Gene ◽  
Common Mechanism ◽  
Prolyl Isomerase ◽  
P53 Signaling ◽  
A Cell ◽  
And Function

Increased survival, differentiation, and apoptotic death are common mechanisms relevant for both cancer and neurodegenerative diseases. Although these disorders are characterized by different manifestations, it appears that a common mechanism may be present which directs the fate of a cell to either degeneration or proliferation. There are two classes of proteins that have been extensively investigated in these diseases but their possible interaction during signal transduction has not been studied. Prolyl isomerase Pin1 is an enzyme which translates Ser/Thr-Pro phosphorylation into conformational changes able to modify the activities of its substrates. Its role in cancer development has been linked to its capacity to induce conformational changes to the tumor suppressor gene p53. Neurotrophins belong to a family of proteins that induce opposite effects on neuronal cells such as increased survival, development, and function. According to their function, alteration of these proteins during neurodegenerative processes has been investigated and reported in a number of experimental paradigms involving animal models and humans. However, in recent years, it has been shown that Pin1 downregulation is present in neurodegenerative disorders, while increased expression of neurotrophins and their receptors is found in certain types of cancer and correlate with poor prognosis. Notably, at the level of signal transduction, Pin1 and neurotrophin activity regulate the outcome of similar pathways such as proline-directed kinase and, most importantly, p53 signaling. Thus the possible existence of a loop between Pin1 and neurotrophins was investigated to understand the pathogenesis of these diseases.

scholarly journals Cell Size Influences the Reproductive Potential and Total Lifespan of theSaccharomyces cerevisiaeYeast as Revealed by the Analysis of Polyploid Strains

2018 ◽  
Vol 2018 ◽  
pp. 1-17 ◽  
Author(s):  
Renata Zadrag-Tecza ◽  
Magdalena Kwolek-Mirek ◽  
Małgorzata Alabrudzińska ◽  
Adrianna Skoneczna
Keyword(s):  
Cell Death ◽  
Cell Size ◽  
Reproductive Potential ◽  
Threshold Value ◽  
Yeast Cells ◽  
Common Mechanism ◽  
A Cell ◽  
Genome Copy Number ◽  
The Difference ◽  
Two Phases

The total lifespan of the yeastSaccharomyces cerevisiaemay be divided into two phases: the reproductive phase, during which the cell undergoes mitosis cycles to produce successive buds, and the postreproductive phase, which extends from the last division to cell death. These phases may be regulated by a common mechanism or by distinct ones. In this paper, we proposed a more comprehensive approach to reveal the mechanisms that regulate both reproductive potential and total lifespan in cell size context. Our study was based on yeast cells, whose size was determined by increased genome copy number, ranging from haploid to tetraploid. Such experiments enabled us to test the hypertrophy hypothesis, which postulates that excessive size achieved by the cell—the hypertrophy state—is the reason preventing the cell from further proliferation. This hypothesis defines the reproductive potential value as the difference between the maximal size that a cell can reach and the threshold value, which allows a cell to undergo its first cell cycle and the rate of the cell size to increase per generation. Here, we showed that cell size has an important impact on not only the reproductive potential but also the total lifespan of this cell. Moreover, the maximal cell size value, which limits its reproduction capacity, can be regulated by different factors and differs depending on the strain ploidy. The achievement of excessive size by the cell (hypertrophic state) may lead to two distinct phenomena: the cessation of reproduction without “mother” cell death and the cessation of reproduction with cell death by bursting, which has not been shown before.

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