Perinatal findings in a patient with a novel large chromosome 19p deletion

Abstract Background Lupins are cultivated as human consumption grains and forage legumes. The chromosomes of lupins are too small to be karyotyped by conventional techniques, because they reveal a general lack of distinctive cytological features. In the current study, Fluorescence in situ Hybridization (FISH) was used to locate 5S and 45S ribosomal gene sites on the chromosomes of Lupinus albus ssp albus, Lupinus albus ssp graecus, Lupnus termis (all with 2n = 50), and Lupinus polyphyllus lindl var. polyphyllus (2n = 48), FISH together with seed storage protein electrophoretic patterns were used to find out the relationship among these species. Results The double-target FISH on the chromosomes of the studied species with rDNA probes revealed that the two types of rRNA genes are located on different chromosomes. The detected loci of rRNA genes partially reflected the taxonomical similarity among the two Lupinus albus subspecies and L. termis. Lupinus polyphyllus lindl var. polyphyllus was exception by having unique large chromosome mostly is covered by one signal of 45S rDNA, whereas its homologous chromosome seems to be normal-sized and have the other 45S rDNA locus. The similarity matrix among the Lupinus species as computed according to Jaccardʼs Coefficient from the SDS-PAGE, showed that L. albus ssp. Albus and L. albus ssp. Graecus are the most similar species (~ 97%), and then comes L. termis, and L. polyphyllus lindl var. polyphylus has been placed in separate clade and still the most related species to it among the studied species is L. termis (~ 70%). Conclusion It could be postulated from FISH and seed storage protein electrophoretic patterns that the relationships among the studied species is as follows, Lupinus albus ssp albus, is the most related species to Lupinus albus ssp graecus then comes Lupnus termis and Lupinus polyphyllus lindl var. polyphyllus at a distal position.

Download Full-text

Cellular oncogenes (c-erb-A and c-erb-B) located on different chicken chromosomes can be transduced into the same retroviral genome

Molecular and Cellular Biology ◽

10.1128/mcb.4.8.1627-1630.1984 ◽

1984 ◽

Vol 4 (8) ◽

pp. 1627-1630

Author(s):

G Symonds ◽

E Stubblefield ◽

M Guyaux ◽

J M Bishop

Keyword(s):

Chicken Genome ◽

Large Chromosome ◽

Cellular Genes ◽

Intermediate Size ◽

Avian Erythroblastosis Virus ◽

Cellular Oncogenes

Avian erythroblastosis virus has transduced two cellular genes, c-erb-A and c-erb-B. Using fractionated chicken chromosomes, we found that the two genes are located on different chromosomes in the chicken genome: c-erb-A is on a microchromosome, and c-erb-B is on a large chromosome. The locations of two other cellular oncogenes (c-fps and c-myb) were also determined: c-fps is on a microchromosome, and c-myb is on chromosome of an intermediate size. Our results suggest that avian erythroblastosis virus had transduced the two cellular genes independently, conforming to previous indications that cellular oncogenes are dispersed among multiple chromosomes in every species that has been examined.

Download Full-text

Chromosomal analyses in Megalonema platanum (Siluriformes: Pimelodidae), an endangered species from South American rivers

Neotropical Ichthyology ◽

10.1590/s1679-62252011005000008 ◽

2011 ◽

Vol 9 (1) ◽

pp. 177-182 ◽

Cited By ~ 6

Author(s):

Rafael Augusto de Carvalho ◽

Sebástian Sanchez ◽

Ana Claudia Swarça ◽

Alberto Sergio Fenocchio ◽

Isabel C. Martins-Santos ◽

...

Keyword(s):

Diploid Number ◽

Secondary Constriction ◽

Centromeric Heterochromatin ◽

Large Chromosome ◽

South American ◽

Terminal Position ◽

Chromosomal Data ◽

First Time ◽

Secondary Constrictions ◽

Submetacentric Pair

This study presents chromosomal data of Megalonema platanum from rio Tibagi, Paraná, Brazil and from rio Paraná, Argentina. The diploid number was equal 54 with karyotype composition of 24m+16sm+2st+12a in both populations. The AgNOR sites were detected in the terminal position of a submetacentric pair of the two analyzed populations, coinciding with secondary constrictions on the short arm of pair 15. CMA3 and FISH with 18S rDNA probe displayed fluorescent signals that correspond to the AgNOR sites and secondary constriction. The presence of a small acrocentric supernumerary chromosome can be observed in M. platanum from rio Tibagi, with centromeric heterochromatin. Others heterochromatic blocks were evidenced in the terminal position of some chromosome and one metacentric large chromosome pair, probably the first pair, showed an interstitial heterochromatin. In the population of the rio Paraná were still observed heterochromatic blocks in both ends in some chromosomes. This work brings for the first time cytogenetic date of M. platanum, which is a very rare species in the rio Paraná basin and may be endangered.

Download Full-text

A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance

10.1101/2020.08.22.256727 ◽

2020 ◽

Author(s):

Tyler W. Doughty ◽

Rosemary Yu ◽

Lucy Fang-I Chao ◽

Zhongjun Qin ◽

Verena Siewers ◽

...

Keyword(s):

Carbon Source ◽

Reference Strain ◽

Biomass Concentration ◽

Biomass Accumulation ◽

Ethanol Metabolism ◽

Large Chromosome ◽

Lag Phase ◽

Diauxic Shift ◽

Single Chromosome ◽

Genome Arrangement

AbstractThis study characterized the growth, metabolism, and transcriptional profile of a S. cerevisiae strain with a single large chromosome that was constructed via successive chromosomal fusions. The single chromosome strain exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a wildtype strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed diminished induction of genes involved in diauxic shift, ethanol metabolism, fatty-acid ß-oxidation, and methylglyoxal catabolism during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling predicted that decreased flux through these poorly induced enzymes results in diminished ATP formation and decreased biomass accumulation observed. Together, these observations suggest that switch-like control of carbon source dependent gene expression in S. cerevisiae requires genome arrangement into multiple chromosomes.

Download Full-text

Periodic variation of mutation rates in bacterial genomes associated with replication timing

10.1101/195818 ◽

2017 ◽

Author(s):

Marcus M. Dillon ◽

Way Sung ◽

Michael Lynch ◽

Vaughn S. Cooper

Keyword(s):

Vibrio Fischeri ◽

Bacterial Species ◽

Replication Timing ◽

Small Chromosome ◽

Burkholderia Cenocepacia ◽

Mutation Rates ◽

Base Substitution ◽

Large Chromosome ◽

Bacterial Genomes ◽

Substitution Mutation

ABSTRACTThe causes and consequences of spatiotemporal variation in mutation rates remains to be explored in nearly all organisms. Here we examine relationships between local mutation rates and replication timing in three bacterial species whose genomes have multiple chromosomes:Vibrio fischeri, Vibrio cholerae, andBurkholderia cenocepacia. Following five evolution experiments with these bacteria conducted in the near-absence of natural selection, the genomes of clones from each lineage were sequenced and analyzed to identify variation in mutation rates and spectra. In lineages lacking mismatch repair, base-substitution mutation rates vary in a mirrored wave-like pattern on opposing replichores of the large chromosome ofV. fischeriandV. cholerae, where concurrently replicated regions experience similar base-substitution mutation rates. The base-substitution mutation rates on the small chromosome are less variable in both species but occur at similar rates as the concurrently replicated regions of the large chromosome. Neither nucleotide composition nor frequency of nucleotide motifs differed among regions experiencing high and low base-substitution rates, which along with the inferred ~800 Kb wave period suggests that the source of the periodicity is not sequence-specific but rather a systematic process related to the cell cycle. These results support the notion that base-substitution mutation rates are likely to vary systematically across many bacterial genomes, which exposes certain genes to elevated deleterious mutational load.

Download Full-text

Parental infections disrupt clustered genes encoding related functions required for nervous system development in newborns

10.1101/448845 ◽

2018 ◽

Author(s):

Bernard Friedenson

Keyword(s):

Dna Sequences ◽

Neurodevelopmental Disorders ◽

Neurodevelopmental Disorder ◽

Gene Clusters ◽

Nervous System Development ◽

Driver Mutations ◽

Large Chromosome ◽

Chromosomal Anomalies ◽

Chromosome Anomalies ◽

Human Dna

AbstractThe purpose of this study was to understand the role of infection in the origin of chromosomal anomalies linked to neurodevelopmental disorders. In children with disorders in the development of their nervous systems, chromosome anomalies known to cause these disorders were compared to viruses and bacteria including known teratogens. Results support the explanation that parental infections disrupt elaborate multi-system gene coordination needed for neurodevelopment. Genes essential for neurons, lymphatic drainage, immunity, circulation, angiogenesis, cell barriers, structure, and chromatin activity were all found close together in polyfunctional clusters that were deleted in neurodevelopmental disorders. These deletions account for immune, circulatory, and structural deficits that accompany neurologic deficits. In deleted gene clusters, specific and repetitive human DNA matched infections and passed rigorous artifact tests. In some patients, epigenetic driver mutations were found and may be functionally equivalent to deleting a cluster or changing topologic chromatin interactions because they change access to large chromosome segments. In three families, deleted DNA sequences were associated with intellectual deficits and were not included in any database of genomic variants. These sequences were thousands of bp and unequivocally matched foreign DNAs. Analogous homologies were also found in chromosome anomalies of a recurrent neurodevelopmental disorder. Viral and bacterial DNAs that match repetitive or specific human DNA segments are thus proposed to interfere with highly active break repair during meiosis; sometimes delete polyfunctional clusters, and disable epigenetic drivers. Mis-repaired gametes produce zygotes containing rare chromosome anomalies which cause neurologic disorders and accompanying non-neurologic signs. Neurodevelopmental disorders may be examples of assault on the human genome by foreign DNA with some infections more likely tolerated because they resemble human DNA segments. Further tests of this model await new technology.Graphic Abstract

Download Full-text

Otolith?Ocular responses in familial episodic ataxia linked to chromosome 19p

Annals of Neurology ◽

10.1002/ana.410420209 ◽

1997 ◽

Vol 42 (2) ◽

pp. 189-193 ◽

Cited By ~ 2

Author(s):

Joseph M. Furman

Keyword(s):

Episodic Ataxia ◽

Chromosome 19P

Download Full-text

Single-copy and amplified CAD genes in Syrian hamster chromosomes localized by a highly sensitive method for in situ hybridization

Molecular and Cellular Biology ◽

10.1128/mcb.2.3.308-319.1982 ◽

1982 ◽

Vol 2 (3) ◽

pp. 308-319

Author(s):

G M Wahl ◽

L Vitto ◽

R A Padgett ◽

G R Stark

Keyword(s):

In Situ Hybridization ◽

Syrian Hamster ◽

Specific Radioactivity ◽

Large Chromosome ◽

Hybridization Technique ◽

Wild Type ◽

Aspartate Transcarbamylase ◽

Metaphase Chromosomes ◽

Cad Gene

Syrian hamster cells resistant to N-(phosphonacetyl)-L-aspartate (PALA), a specific inhibitor of the aspartate transcarbamylase activity of the multifunctional protein CAD, overproduce this protein as a result of amplification of the CAD gene. We have used a sensitive in situ hybridization technique to localize CAD genomes in spreads of metaphase chromosomes from several independent PALA-resistant lines and from wild-type PALA-sensitive cells. The amplified genes were always found within chromosomes, usually in an expanded region of the short arm of chromosome B9. In wild-type cells, the CAD gene was also on the short arm of chromosome B9. In one mutant line, 90 to 100 CAD genes were found within an expanded B9 chromosome and 10 to 15 more were near the distal end of one arm of several different chromosomes. Another line contained most the genes in a telomeric chromosome or large chromosome fragment. The amplified genes were in chromosomal regions that were stained in a banded pattern by trypsin-Giemsa. A few double minute chromosomes were observed in a very small fraction of the total spreads examined. The it situ hybridizations were performed in the presence of 10% dextral sulfate 500, which increases the signal by as much as 100-fold. Using recombinant DNA plasmids nick-translated with [125I]dCTP to high specific radioactivity, 10 CAD genes in a single chromosomal region were revealed after 1 week of autoradiographic exposure, and the position of the unique gene could be seen after 1 month.

Download Full-text

Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016

Journal of Medical Microbiology ◽

10.1099/jmm.0.001443 ◽

2021 ◽

Vol 70 (11) ◽

Author(s):

Mark Philip Bugayong ◽

Hidemasa Izumiya ◽

Josie M. Bilar ◽

Masatomo Morita ◽

Eiji Arakawa ◽

...

Keyword(s):

Vibrio Cholerae ◽

Type Species ◽

Variable Number Tandem Repeat ◽

The Philippines ◽

Large Chromosome ◽

Content Type ◽

Link Type ◽

Mlva Type ◽

El Tor

Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies. Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines. Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping. Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries. Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.

Download Full-text

Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids

BMC Genomics ◽

10.1186/s12864-020-07221-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Chia-Chi Hsu ◽

Shu-Yun Chen ◽

Pei-Han Lai ◽

Yu-Yun Hsiao ◽

Wen-Chieh Tsai ◽

...

Keyword(s):

Homologous Recombination ◽

Long Terminal Repeat ◽

Genome Size ◽

Copy Number ◽

Terminal Repeat ◽

26S Proteasome ◽

Large Chromosome ◽

Genome Sequences ◽

Copper Transporter ◽

Expression Levels

Abstract Background Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure. Results We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions. Conclusion Orchid-rt1 and Gypsy1–3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.

Download Full-text