scholarly journals Unequal signal and coding joint formation in human V(D)J recombination.

1993 ◽  
Vol 13 (7) ◽  
pp. 3900-3906 ◽  
Author(s):  
G H Gauss ◽  
M R Lieber
Keyword(s):  
Cell Lines ◽  
Relative Efficiency ◽  
Chromosomal Rearrangements ◽  
The Other ◽  
Combined Effects ◽  
Recombination Activity ◽  
Coding Sequences ◽  
Joint Formation ◽  
Differential Reaction ◽  
Endogenous Loci

Substrates for studying V(D)J recombination in human cells and two human pre-B-cell lines that have active V(D)J recombination activity are described. Using these substrates, we have been able to analyze the relative efficiency of signal joint and coding joint formation. Coding joint formation was five- to sixfold less efficient than signal joint formation in both cell lines. This imbalance between the two halves of the reaction was demonstrated on deletional substrates, where each joint is assayed individually. In both cell lines, the inversional reaction (which requires formation of both a signal and a coding joint) was more than 20-fold less efficient than signal joint formation alone. The signal and coding sequences are identical in all of these substrates. Hence, the basis for these differential reaction ratios appears to be that coding joint and signal joint formation are both inefficient and their combined effects are such that inversions (two-joint reactions) reflect the product of these inefficiencies. Physiologically, these results have two implications. First, they show how signal and coding joint formation efficiencies can affect the ratio of deletional to inversional products at endogenous loci. Second, the fact that not all signal and coding joints go to completion implies that the recombinase is generating numerous broken ends. Such unresolved ends may participate in pathologic chromosomal rearrangements even when the other half of the same reaction may have proceeded to resolution.

Unequal signal and coding joint formation in human V(D)J recombination

1993 ◽  
Vol 13 (7) ◽  
pp. 3900-3906
Author(s):  
G H Gauss ◽  
M R Lieber
Keyword(s):  
Cell Lines ◽  
Relative Efficiency ◽  
Chromosomal Rearrangements ◽  
The Other ◽  
Combined Effects ◽  
Recombination Activity ◽  
Coding Sequences ◽  
Joint Formation ◽  
Differential Reaction ◽  
Endogenous Loci

Substrates for studying V(D)J recombination in human cells and two human pre-B-cell lines that have active V(D)J recombination activity are described. Using these substrates, we have been able to analyze the relative efficiency of signal joint and coding joint formation. Coding joint formation was five- to sixfold less efficient than signal joint formation in both cell lines. This imbalance between the two halves of the reaction was demonstrated on deletional substrates, where each joint is assayed individually. In both cell lines, the inversional reaction (which requires formation of both a signal and a coding joint) was more than 20-fold less efficient than signal joint formation alone. The signal and coding sequences are identical in all of these substrates. Hence, the basis for these differential reaction ratios appears to be that coding joint and signal joint formation are both inefficient and their combined effects are such that inversions (two-joint reactions) reflect the product of these inefficiencies. Physiologically, these results have two implications. First, they show how signal and coding joint formation efficiencies can affect the ratio of deletional to inversional products at endogenous loci. Second, the fact that not all signal and coding joints go to completion implies that the recombinase is generating numerous broken ends. Such unresolved ends may participate in pathologic chromosomal rearrangements even when the other half of the same reaction may have proceeded to resolution.

Determination of the Number of Conserved Chromosomal Segments Between Species

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1387-1395 ◽  
Author(s):  
Sudhir Kumar ◽  
Sudhindra R Gadagkar ◽  
Alan Filipski ◽  
Xun Gu
Keyword(s):  
Statistical Approach ◽  
Common Ancestor ◽  
Chromosomal Rearrangements ◽  
Structural Similarity ◽  
The Other ◽  
Segment Length ◽  
Human Genomes ◽  
Genomic Divergence ◽  
Human And Mouse

AbstractGenomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 ± 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of ∼1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only ∼0.74 rearrangements per million years.

scholarly journals Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines.

1991 ◽  
Vol 11 (4) ◽  
pp. 1854-1860 ◽  
Author(s):  
N P Shah ◽  
O N Witte ◽  
C T Denny
Keyword(s):  
Transcription Factor ◽  
Cell Lines ◽  
Transcription Initiation ◽  
Transcriptional Control ◽  
Philadelphia Chromosome ◽  
Gc Content ◽  
Cellular Transformation ◽  
Nucleotide Sequence Analysis ◽  
Coding Sequences ◽  
Gene Assay

The t(9;22) Philadelphia chromosome translocation fuses 5' regulatory and coding sequences of the BCR gene to the c-ABL proto-oncogene. This results in the formation of hybrid BCR-ABL mRNAs and proteins. The shift in ABL transcriptional control to the BCR promoter may play a role in cellular transformation mediated by this rearrangement. We have functionally localized the BCR promoter to a region 1 kb 5' of BCR exon 1 coding sequences by using a chloramphenicol acetyltransferase reporter gene assay. Nucleotide sequence analysis of this region revealed many consensus binding sequences for transcription factor SP1 as well as two potential CCAAT box binding factor sites and one putative helix-loop-helix transcription factor binding site. No TATA-like or "initiator" element sequences were found. Because of low steady-state levels of BCR mRNA and the high GC content (78%) of the promoter region, definitive mapping of transcription start sites required artificial amplification of BCR promoter-directed transcripts. Overexpression from the BCR promoter in a COS cell system was effective in demonstrating multiple transcription initiation sites. In order to assess the effects of chromosomal translocation on the transcriptional control of the BCR gene, we determined S1 nuclease protection patterns of poly(A)+ RNA from tumor cell lines. No differences were observed in the locations and levels of BCR transcription initiation sites between those lines that harbored the t(9;22) translocation and those that did not. This demonstrates that BCR promoter function remains intact in spite of genomic rearrangement. The BCR promoter is structurally similar to the ABL promoters. Together, this suggests that the structural fusion of BCR-ABL and not its transcriptional deregulation is primarily responsible for the transforming effect of the t(9;22) translocation.

Bioelectronic Sensor Technology for Detection of Cystic Fibrosis and Hereditary Hemochromatosis Mutations

2003 ◽  
Vol 127 (12) ◽  
pp. 1565-1572
Author(s):  
Susan H. Bernacki ◽  
Daniel H. Farkas ◽  
Wenmei Shi ◽  
Vivian Chan ◽  
Yenbou Liu ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Genetic Testing ◽  
Cell Lines ◽  
Molecular Genetic ◽  
Hereditary Hemochromatosis ◽  
The Other ◽  
Molecular Diagnostic ◽  
Molecular Genetic Testing ◽  
Diagnostic Applications ◽  
Lymphocyte Cell

Abstract Context.—Bioelectronic sensors, which combine microchip and biological components, are an emerging technology in clinical diagnostic testing. An electronic detection platform using DNA biochip technology (eSensor) is under development for molecular diagnostic applications. Owing to the novelty of these devices, demonstrations of their successful use in practical diagnostic applications are limited. Objective.—To assess the performance of the eSensor bioelectronic method in the validation of 6 Epstein-Barr virus–transformed blood lymphocyte cell lines with clinically important mutations for use as sources of genetic material for positive controls in clinical molecular genetic testing. Two cell lines carry mutations in the CFTR gene (cystic fibrosis), and 4 carry mutations in the HFE gene (hereditary hemochromatosis). Design.—Samples from each cell line were sent for genotype determination to 6 different molecular genetic testing facilities, including the laboratory developing the DNA biochips. In addition to the bioelectronic method, at least 3 different molecular diagnostic methods were used in the analysis of each cell line. Detailed data were collected from the DNA biochip output, and the genetic results were compared with those obtained using the more established methods. Results.—We report the successful use of 2 applications of the bioelectronic platform, one for detection of CFTR mutations and the other for detection of HFE mutations. In all cases, the results obtained with the DNA biochip were in concordance with those reported for the other methods. Electronic signal output from the DNA biochips clearly differentiated between mutated and wild-type alleles. This is the first report of the use of the cystic fibrosis detection platform. Conclusions.—Bioelectronic sensors for the detection of disease-causing mutations performed well when used in a “real-life” situation, in this case, a validation study of positive control blood lymphocyte cell lines with mutations of public health importance. This study illustrates the practical potential of emerging bioelectronic DNA detection technologies for use in current molecular diagnostic applications.

Paranemin and the organization of desmin filament networks

2001 ◽  
Vol 114 (6) ◽  
pp. 1079-1089 ◽  
Author(s):  
S.C. Schweitzer ◽  
M.W. Klymkowsky ◽  
R.M. Bellin ◽  
R.M. Robson ◽  
Y. Capetanaki ◽  
...  
Keyword(s):  
Cell Lines ◽  
Intermediate Filament ◽  
Transgene Expression ◽  
De Novo ◽  
Muscle Cells ◽  
The Other ◽  
Intermediate Filament Proteins ◽  
Mouse Fibroblasts ◽  
Filament Networks ◽  
Filament Network

De novo expression of vimentin, GFAP or peripherin leads to the assembly of an extended intermediate filament network in intermediate filament-free SW13/cl.2 cells. Desmin, in contrast, does not form extended filament networks in either SW13/cl.2 or intermediate filament-free mouse fibroblasts. Rather, desmin formed short thickened filamentous structures and prominent spot-like cytoplasmic aggregates that were composed of densely packed 9–11 nm diameter filaments. Analysis of stably transfected cell lines indicates that the inability of desmin to form extended networks is not due to a difference in the level of transgene expression. Nestin, paranemin and synemin are large intermediate filament proteins that coassemble with desmin in muscle cells. Although each of these large intermediate filament proteins colocalized with desmin when coexpressed in SW-13 cells, expression of paranemin, but not synemin or nestin, led to the formation of an extended desmin network. A similar rescue of desmin network organization was observed when desmin was coexpressed with vimentin, which coassembles with desmin, or with keratins, which formed a distinct filament network. These studies demonstrate that desmin filaments differ in their organizational properties from the other vimentin-like intermediate filament proteins and appear to depend upon coassembly with paranemin, at least when they are expressed in non-muscle cells, in order to form an extended filament network.

CHROMOSOMES AND DNA OF MICROTUS II. CONFIRMATION OF DELETION OF CONSTITUTIVE HETEROCHROMATIN IN M. AGRESTIS CELLS IN VITRO

1977 ◽  
Vol 19 (3) ◽  
pp. 537-541 ◽  
Author(s):  
J. E. K. Cooper
Keyword(s):  
Somatic Cell ◽  
Cell Line ◽  
Cell Lines ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Constitutive Heterochromatin ◽  
The Other ◽  
Microtus Agrestis ◽  
C Banding

The distribution of constitutive heterochromatin has been examined by C-banding in two somatic cell lines, grown in vitro, from a female Microtus agrestis. One line retains one intact X chromosome together with the short arm of the other X chromosome, while the other cell line retains only the short arm of one X chromosome. Thus, each cell line has lost substantial amounts of heterochromatin from the sex chromosomes, but this material has been deleted from the cells, and not translocated to other chromosomes. Nonetheless, both cell lines continue to propagate well in vitro.

scholarly journals Consistency of in vitro drug sensitivities within pharmacological classes

2021 ◽  
Vol 15 (1) ◽  
pp. 12
Author(s):  
Casey Hon ◽  
Sisira Nair ◽  
Petr Smirnov ◽  
Hossein Sharifi-Noghabi ◽  
Nikta Feizi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Cancer Therapeutics ◽  
The Other ◽  
Comparative Analyses ◽  
Potential Sources ◽  
The Common ◽  
Pharmacogenomic Studies

Multiple comparative analyses between the common drugs and cell lines of the Genomics of Drug Sensitivity in Cancer (GDSC) and the Cancer Therapeutics Response Portal (CTRP) have previously shown low consistency between the in vitro phenotypic measures of a drug in one study with the other. While several potential sources of inconsistency have been tested, the similar targets of tested compounds has yet to be tested as a contributing factor of discrepancy. This analysis includes two methods of reclassifying drugs into classes based on their targets to identify the truer set of consistent cell lines, showing an increased correlation between the two pharmacogenomic studies.

scholarly journals PENGUKURAN EFISIENSI AGROINDUSTRI PANGAN LOKAL ENBAL DENGAN PENDEKATAN DATA ENVELOPMENT ANALYSIS

2017 ◽  
Vol 13 (1) ◽  
pp. 1
Author(s):  
Natelda R Timisela ◽  
Ester D Leatemia ◽  
Febby J Polnaya ◽  
Rachel Breemer
Keyword(s):  
Data Envelopment Analysis ◽  
Relative Efficiency ◽  
Production Cost ◽  
Efficiency Analysis ◽  
The Other ◽  
Data Envelopment ◽  
Sago Starch ◽  
Good Efficiency ◽  
Business Efficiency ◽  
Production Increase

The current research aimed to analyze the relative efficiency level of enbal (sago starch) agro-industries. The relative efficiency analysis on 32 DMUs of enbal agro-industries showed that 40,63% of the industries were efficient and 59.38% were inefficient. Every efficient DMU became the reference for the inefficient DMUs based on the suggested quality. Each DMU of the enbal agro-industries has not reached a good efficiency level, which was indicated by the average relative efficiency scale of 0.886. This was a relatively low value, and improvements on the use of production input were needed. The analysis result on the DMUs of the enbal agro-industries which were on constant return to scale position were 40,62%. This showed that enbal agro-industries actors have applied production input efficiently, for the production increase was equal to the use of input. In other words, the use of input was more proportional. The DMUs of enbal agro-industries which were on decreasing return to scale position were 15,63%. This showed that the use of production input had been unsuitable so that the output decreases and the production cost increased. Meanwhile, the DMUs that were on increasing return to scale position were 43,75%. This showed that the industry actors who used certain production input would create efficient DMUs. On the other hand, the input excess would possibly decrease the output. As a result, the industry actors should be concerned about the use of production input in order to establish business efficiency.

scholarly journals Contrasting effects of the onset of spring on reproductive success of Arctic-nesting geese

The Auk ◽  
2019 ◽  
Vol 137 (1) ◽  
Author(s):  
Bart A Nolet ◽  
Kees H T Schreven ◽  
Michiel P Boom ◽  
Thomas K Lameris
Keyword(s):  
Population Dynamics ◽  
Late Onset ◽  
The Other ◽  
Second Phase ◽  
Combined Effects ◽  
Negative Effects ◽  
Early Snowmelt ◽  
The One ◽  
Winter Flocks ◽  
Breeding Propensity

Abstract Breeding output of geese, measured as the proportion of juveniles in autumn or winter flocks, is lower in years with a late onset of spring in some species, but higher in at least one other species. Here we argue that this is because the timing of spring affects different stages of the reproductive cycle differently in different species. Because the effects on 2 different stages are opposite, the combined effects can result in either a positive or a negative overall effect. These stages are the pre-laying, laying, and nesting phase on the one hand; and the hatchling, fledgling, and juvenile phase on the other hand. The first phase is predominantly positively affected by an early snowmelt, with higher breeding propensity, clutch size, and nest success. The second phase in contrast is negatively affected by early snowmelt because of a mismatch with a nutrient food peak, leading to slow gosling growth and reduced survival. We argue that recognition of this chain of events is crucial when one wants to predict goose productivity and eventually goose population dynamics. In a rapidly warming Arctic, the negative effects of a mismatch might become increasingly important.

scholarly journals Establishment of a novel human CIC-DUX4 sarcoma cell line, Kitra-SRS, with autocrine IGF-1R activation and metastatic potential to the lungs

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sho Nakai ◽  
Shutaro Yamada ◽  
Hidetatsu Outani ◽  
Takaaki Nakai ◽  
Naohiro Yasuda ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Fusion Gene ◽  
Primary Tumour ◽  
Chromosomal Rearrangements ◽  
Basic Research ◽  
Metastatic Potential ◽  
Original Tumour

Abstract Approximately 60–70% of EWSR1-negative small blue round cell sarcomas harbour a rearrangement of CIC, most commonly CIC-DUX4. CIC-DUX4 sarcoma (CDS) is an aggressive and often fatal high-grade sarcoma appearing predominantly in children and young adults. Although cell lines and their xenograft models are essential tools for basic research and development of antitumour drugs, few cell lines currently exist for CDS. We successfully established a novel human CDS cell line designated Kitra-SRS and developed orthotopic tumour xenografts in nude mice. The CIC-DUX4 fusion gene in Kitra-SRS cells was generated by t(12;19) complex chromosomal rearrangements with an insertion of a chromosome segment including a DUX4 pseudogene component. Kitra-SRS xenografts were histologically similar to the original tumour and exhibited metastatic potential to the lungs. Kitra-SRS cells displayed autocrine activation of the insulin-like growth factor 1 (IGF-1)/IGF-1 receptor (IGF-1R) pathway. Accordingly, treatment with the IGF-1R inhibitor, linsitinib, attenuated Kitra-SRS cell growth and IGF-1-induced activation of IGF-1R/AKT signalling both in vitro and in vivo. Furthermore, upon screening 1134 FDA-approved drugs, the responses of Kitra-SRS cells to anticancer drugs appeared to reflect those of the primary tumour. Our model will be a useful modality for investigating the molecular pathology and therapy of CDS.

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