Extra Chromosomal Material Research Articles

Gene Silencing and Gene Delivery in Therapeutics: Insights Using Quantum Dots.

Hemophilia, cancer, diabetes, cardiovascular disease, mental health issues, immunological deficiencies, neuromuscular disease, blindness, and other ailments can all be treated with gene silencing and gene therapy, a growing discipline in medicine. It typically refers to a range of therapeutic techniques in which a patient's body's particular cells are given genetic material designed to correct and erase genetic flaws. The advancements in genetics and bioengineering have paved the way for the conceptualization of gene therapy through the manipulation of vectors, enabling the targeted transfer of extrachromosomal material to specific cells. One of the main focus areas of this methodology is the escalation of delivery vehicles (vectors), primarily plasmids or viruses; it still has difficulties because there is no good delivery mechanism that can precisely deliver stable small interfering Ribonucleic Acid (siRNA) or DNA to the target tissue location. As they are non-fluorescent, the siRNA or DNA delivery procedure is unable to be monitored by these carriers. In the context of quantum dots (QDs), the formation of QD-siRNA or QD/DNA complexes facilitated the real-time monitoring and precise localization of QDs during the silencing, delivery, and transfection processes. The unique dual-modality optical and fluorescent properties exhibited by quantum dots contribute to their utility as versatile imaging probes. The research studies discussed in this review article will provide a framework for designing efficient QD-based nanocarriers that can successfully carry therapeutic genetic tools into targeted cells. As a result of their findings, the researchers developed some unique QDs that successfully attached to the siRNA or DNA and carried it to the desired place. The use of these QD-based delivery devices could enhance the field of gene silencing and gene delivery.

Health Supervision for Children and Adolescents With Down Syndrome.

Health Supervision for Children and Adolescents With Down Syndrome.

A rare familial rearrangement of chromosomes 9 and 15 associated with intellectual disability: a clinical and molecular study

BackgroundThere are many reports on rearrangements occurring separately in the regions of chromosomes 9p and 15q affected in the case under study. 15q duplication syndrome is caused by the presence of at least one extra maternally derived copy of the Prader–Willi/Angelman critical region. Trisomy 9p is the fourth most frequent chromosome anomaly with a clinically recognizable syndrome often accompanied by intellectual disability. Here we report a new case of a patient with maternally derived unique complex sSMC resulting in partial trisomy of both chromosomes 9 and 15 associated with intellectual disability.Case presentationWe characterise a supernumerary derivative chromosome 15: 47,XY,+der(15)t(9;15)(p21.2;q13.2), likely resulting from 3:1 malsegregation during maternal gametogenesis. Chromosomal analysis showed that a phenotypically normal mother is a carrier of balanced translocation t(9;15)(p21.1;q13.2). Her 7-year-old son showed signs of intellectual disability and a number of physical abnormalities including bilateral cryptorchidism and congenital megaureter. The child’s magnetic resonance imaging showed changes in brain volume and in structural and functional connectivity revealing phenotypic changes caused by the presence of the extra chromosome material, whereas the mother’s brain MRI was normal. Sequence analyses of the microdissected der(15) chromosome detected two breakpoint regions: HSA9:25,928,021-26,157,441 (9p21.2 band) and HSA15:30,552,104-30,765,905 (15q13.2 band). The breakpoint region on chromosome HSA9 is poor in genetic features with several areas of high homology with the breakpoint region on chromosome 15. The breakpoint region on HSA15 is located in the area of a large segmental duplication.ConclusionsWe discuss the case of these phenotypic and brain MRI features in light of reported signatures for 9p partial trisomy and 15 duplication syndromes and analyze how the genomic characteristics of the found breakpoint regions have contributed to the origin of the derivative chromosome. We recommend MRI for all patients with a developmental delay, especially in cases with identified rearrangements, to accumulate more information on brain phenotypes related to chromosomal syndromes.

Detection of integron genes in the plasmid DNA of multidrug resistant Pseudomonas aeruginosa isolated from surgical wounds of some patients in Benin City, Nigeria

Pseudomonas aeruginosa is an opportunistic pathogen with the capability to cause serious surgical wound infections and remains a major healthcare problem. Plasmid is an extra chromosomal material in bacterial cells and confers resistance to the cell against many antibiotics. Genetic elements such as integron are implicated in conferring multidrug resistance (MDR) to P. aeruginosa . This study aims at investigating the occurrence of integron genes (int1, int2, int3) in the plasmid DNA and their ability to cause MDR in P. aeruginosa . In total, 284 different wound swabs were collected, P. aeruginosa isolated and screened using standard laboratory methods. Antibiotics susceptibility tests were carried out using Kirby-Bauer disk diffusion method. Polymerase chain reaction (PCR) was also carried out using P. aeruginosa plasmid DNA as a template to detect the presence/absence of the integron genes using different pairs of specific primers. The results reveal that 34 (54.8%) of the microbes isolated were P. aeruginosa . Most of the isolates showed notable resistance to antibiotics, most notably against Ceftazidime, Augmentin, Cefixime and Gentamicin . Eleven isolates harbors the plasmid DNA . PCR amplification showed that 6 (54.5%) of the P. aeruginosa isolates harbor integron class 1 genes, non harbors the integron class 2 genes while 3 (27.3%) possess the integron class 3 genes. The isolates with these genes were highly resistant to most of the antibiotics used. int1 gene was prevalent then int3.
 Keywords: Antimicrobial, Wound infection, Integron, Polymerase chain reaction, Plasmid DNA

Gene therapy: advances, challenges and perspectives.

ABSTRACTThe ability to make site-specific modifications to the human genome has been an objective in medicine since the recognition of the gene as the basic unit of heredity. Thus, gene therapy is understood as the ability of genetic improvement through the correction of altered (mutated) genes or site-specific modifications that target therapeutic treatment. This therapy became possible through the advances of genetics and bioengineering that enabled manipulating vectors for delivery of extrachromosomal material to target cells. One of the main focuses of this technique is the optimization of delivery vehicles (vectors) that are mostly plasmids, nanostructured or viruses. The viruses are more often investigated due to their excellence of invading cells and inserting their genetic material. However, there is great concern regarding exacerbated immune responses and genome manipulation, especially in germ line cells. In vivo studies in in somatic cell showed satisfactory results with approved protocols in clinical trials. These trials have been conducted in the United States, Europe, Australia and China. Recent biotechnological advances, such as induced pluripotent stem cells in patients with liver diseases, chimeric antigen receptor T-cell immunotherapy, and genomic editing by CRISPR/Cas9, are addressed in this review.

Genomic and physiological characterization of a laboratory-isolated Acinetobacter schindleri ACE strain that quickly and efficiently catabolizes acetate.

An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001 209 bp with an overall DNA G+C content of 42.9 mol% and six plasmids that account for 266 844 bp of extrachromosomal material. The presence or absence of genes related to carbon catabolism and antibiotic resistance were in agreement with the phenotypic characterization of ACE. This strain grew faster and with a higher biomass yield on acetate than the reference strain Acinetobacter baylyi ADP1. However, ACE did not use aromatic compounds and was unable to grow on common carbon sources, such as glucose, xylose, glycerol or citrate. The gluconeogenic and the catechol pathways are complete in ACE, but compounds that are converted to protocatechuate did not sustain growth since some genes of this pathway are missing. Likewise, this strain could not grow on glucose because it lacks the genes of the Entner-Doudoroff pathway. Minimal inhibitory concentration data showed that ACE was susceptible to most of the antimicrobial agents recommended for the clinical treatment of Acinetobacter spp. Some genes related to a possible human-microbe interaction were found in the ACE genome. ACE is likely to have a low pathogenic risk, as is the case with other A. schindleri strains. These results provide a valuable reference for broadening the knowledge of the biology of Acinetobacter.

Mesophilic strains of Aeromonas spp. can acquire the multidrug resistance plasmid pRAS1 in horizontal transfer experiments at low temperatures

Both biotic and abiotic characteristics of an ecosystem play an important role in the horizontal transfer of DNA in nature. The abiotic factor temperature has a great impact on such transfers as it controls the metabolic activity of mesophilic microorganisms. Moreover, psychrophilic bacteria, which are not affected by low temperatures, are considered to be potential donors of DNA to mesophilic bacteria under temperature stress conditions. In our study, mesophilic Aeromonas spp. strains isolated from fresh fish were genotypically identified and used as recipients in in vitro conjugal transfer experiments using plasmid pRAS1 from psychrophilic strain Aeromonas salmonicida 718 at three different temperatures (8, 15 and 20 °C). The transfer of the plasmid was confirmed by identifying the elements of the integron in pRAS1. A low temperatures did not prevent the transfer of the pRAS1 plasmid to Aeromonas veronii, A. media, A. hydrophila and A. caviae strains, which showed detectable conjugation frequencies of 10–8 at 8 °C. In other strains of the same species, transconjugants were not detected, which indicated that the genetic background of each strain directly affected the ability to be a recipient of this plasmid at the temperatures tested. Our results demonstrate that mesophilic Aeromonas spp. strains are potential reservoirs of extrachromosomal genetic material. Implications of this plasmid transfer at low temperatures and its possible consequences for human health are discussed.

Prenatal diagnosis and molecular cytogenetic characterization of de novo pure partial trisomy 6p associated with microcephaly, craniosynostosis and abnormal maternal serum biochemistry

We present prenatal diagnosis and molecular cytogenetic characterization of de novo pure trisomy 6p22.3→p25.3 encompassing BMP6 in a fetus associated with microcephaly and craniosynostosis on prenatal ultrasound, abnormal maternal serum biochemistry of a low PAPP-A level in the first-trimester combined test, and a karyotype of 46,XX,der(22)t(6;22)(p22.3;p13)dn. The present case demonstrates the usefulness of rapid prenatal identification of the origin of the extra chromosome material on the short arm of an acrocentric chromosome by spectral karyotyping, fluorescence in situ hybridization and array comparative genomic hybridization. We review the phenotypic abnormality of craniosynostosis in previously reported patients with partial trisomy 6p. We discuss the genotype–phenotype correlation of the involved gene of BMP6 in this case.

Complex Chromosome Rearrangement of 6p25.3->p23 and 12q24.32->qter in a Child With Moyamoya

A 7-year-old white girl presented with left hemiparesis and ischemic stroke secondary to moyamoya syndrome, a progressive cerebrovascular occlusive disorder of uncertain but likely multifactorial etiology. Past medical history revealed hearing loss and developmental delay/intellectual disability. Routine karyotype demonstrated extra chromosomal material on 6p. Single nucleotide polymorphism microarray revealed a previously unreported complex de novo genetic rearrangement involving subtelomeric segments on chromosomes 6p and 12q. The duplicated/deleted regions included several known OMIM-annotated genes. This novel phenotype and genotype provides information about a possible association of genomic copy number variation and moyamoya syndrome. Dosage-sensitive genes in the deleted and duplicated segments may be involved in aberrant vascular proliferation. Our case also emphasizes the importance of comprehensive evaluation of both developmental delay and congenital anomalies such as moyamoya.

The downside of ‘inappropriate messaging’: new insight into the development of testicular germ cell tumours in young men?

How invasive testicular germ cell tumours (TGCTs) develop from precursor carcinoma in situ/intratubular germ cell neoplasia unclassified (CIS/IGCNU) cells, and only after puberty, is unknown. In the current issue of The Journal of Pathology, Jørgensen and colleagues have compared the protein expression profile of CIS before and after puberty and in pre-invasive versus invasive TGCT and show that the mitosis-meiosis controller DMRT1 switches off in CIS cells postpubertally and is associated with invasiveness. They also show that CIS cells express a 'confusing' mix of pro- and anti-meiotic proteins; this may predispose CIS cells to accumulate extra chromosomal material which ultimately leads to tumourigenesis.

Polyadenylated RNA and mRNA export factors in extrachromosomal nuclear domains of vitellogenic oocytes in the yellow mealworm Tenebrio molitor

The nucleus of vitellogenic oocytes of the yellow mealworm Tenebrio molitor contains a karyosphere that consists of condensed chromatin embedded in an extrachromosomal fibrogranular material. Numerous nuclear bodies located freely in the nucleoplasm are also observed. Amongst these bodies, counterparts of nuclear speckles (= interchromatin granule clusters (IGCs)) can be identified by the presence of the marker protein SC35. Microinjections of fluorescently tagged 2′-O-Me(U)22 methyl oligoribonucleotide probes, complementary to poly(A) tails of RNAs, revealed poly(A)+ RNA in the vast majority of IGCs. We found that all T. molitor oocyte IGCs contain heterogeneous ribonucleoprotein (hnRNP) core protein A1 localized to IGCs in an RNA-dependent manner. The extrachromosomal material of the karyosphere and some nucleoplasmic IGCs also contain the adapter protein Aly known to provide a link between pre-mRNA splicing and mRNA export. The essential mRNA export factor/receptor NXF1 was colocalized with Aly. In nucleoplasmic IGCs, NXF1 was found to localize in an RNA-dependent manner, whereas it was RNA-independently located in the extrachromosomal material of the karyosphere. We believe our data provide evidence for the implication of nucleoplasmic IGCs in mRNA biogenesis and retention on the path to nuclear export.

The emerging microdeletion and microduplication syndromes: the importance of a diagnosis for both professionals and families

Background and aims Thousands of babies are born each year with errors in the make-up of their chromosomes which can affect their development, learning and behaviour although the effects are variable. These changes frequently constitute a chromosome imbalance: extra or missing chromosome material. Until recently these chromosome aberrations were detected by microscopic karyotype analysis and submicroscopic deletions and duplications were missed. Molecular techniques such as microarray-based comparative genomic hybridisation (arrayCGH) can today identify previously undetectable microdeletions and microduplications, some causing new syndromes. ArrayCGH offers families greater hope of a genetic diagnosis for their child despite the limitations of all genetic tests. The diagnosis of a new syndrome can alert both clinicians and families to future health problems and ensure appropriate screening is in place. Additionally, arrayCGH usually identifies the missing or duplicated genes, potentially improving counselling. Methods Unique is a world-leading support group for families with a rare chromosome disorder (RCD). At November 2011, Unique has over 8,600 member families, representing more than 11,000 individuals. As diagnoses of RCDs increase, membership of Unique is also increasing. Results ArrayCGH offers clinicians faced with a child with non-specific developmental delay, cognitive impairment or challenging behaviour a 20 percent diagnostic rate (compared to 7 percent with karyotype analysis). This has led to a rise of over 100 percent in new members joining Unique annually in the period 2008 to 2010 (the period that arrayCGH was rolled out). For the 870 members joining Unique in November 2010-October 2011 arrayCGH was the most common genetic test used to diagnose their genetic disorder. Many are unique disorders, not previously reported in the medical literature. In response to this, Unique has produced 19 new medically-verified guides on microdeletions and microduplications. Information guides are compiled from the medical literature; from Unique9s database and other publicly available databases; and from detailed surveys completed by member families. Conclusion The rapid increase in diagnosis of RCD made possible by arrayCGH has led to a steep rise in membership of Unique. We continue to publish new information guides in response to this, including newly-emerging microdeletion and microduplication syndromes.

Nine genes that may contribute to partial trisomy (6)(p22→pter) and unique presentation of persistent hyperplastic primary vitreous with retinal detachment

We report on a newborn girl with facial anomalies, a congenital heart defect, severe pre- and postnatal growth retardation, feeding problems, and persistent hyperplastic primary vitreous. Cytogenetic analysis by high resolution GTG banding showed extra chromosomal material on the short arm of one chromosome 1 of the patient, but neither parent. SKY and CGH analysis demonstrated that the patient had a de novo 46,XX, der(1)t(1;6)(p36.3; p22). Compared with previously reported cases of partial trisomy 6p22 syndrome, this patient exhibited a unique condition for this syndrome: persistent hyperplastic primary vitreous (PHPV) with retinal detachment. The human genome database was searched for candidate genes and we propose the following nine genes located in the 6p22→6pter region for their potential contribution to the phenotype of partial trisomy 6p22→pter and persistent hyperplastic primary vitreous (PHPV) with retinal detachment: Forkhead box Q1 (FOXQ1), FOXF2, FOXC1, NRN1, EDN1, ATXN1, DEK oncogene, E2F3, and NRNS1.

Parental karyotype may reveal the source of a pregnancy loss even in the presence of a reportedly euploid fetal karyotype

To present a case of a fetal loss in which a normal fetal karyotype was obtained by banding studies. Identification of an abnormal maternal karyotype prompted subsequent reanalysis using fluorescence in situ hybridization (FISH). Case report. University-affiliated IVF center. A 32-year-old woman, G1 P0, underwent a fetal loss at 8 weeks, and a suction curettage was performed. The patient had a previous first-trimester loss. The fetal tissue was evaluated by banding studies and found to be normal. Parental karyotyping was performed, and the fetal tissue was reanalyzed by FISH. Analysis of fetal karyotype by targeted FISH. Maternal karyotype demonstrated a translocation [46,XX, t(8;10)(q24.3:q25.2)]. The fetal tissue was reanalyzed by FISH, and a segment of chromosome 10 was found on chromosome 8. A normal fetal karyotype, as measured by banding, does not exclude a genetic etiology for pregnancy loss. In this case, maternal translocation prompted the genetics laboratory to search for a small segment of translocated extra chromosomal material. This demonstrated that despite the finding of a normal fetal karyotype, in some cases parental karyotyping may have value.

Phenotypic discordance upon paternal or maternal transmission of duplications of the 11p15 imprinted regions

We report on two families in which the parental origin of duplications of the BWS imprinted regions on chromosome 11p15 influences the phenotype. In family A the transmission of a t(4; 11)(q35; p15.5) translocation results in duplication of BWSIC1 and BWSIC2. If this duplication is transmitted from the father, the extra chromosomal material has the paternal imprint. This results in overexpression of IGF2 and consequently an overgrowth phenotype. If the duplication is transmitted from the mother, the extra chromosomal material has the maternal imprint, resulting in overexpression of CDKN1C and a growth retardation phenotype. In family B an interstitial duplication of BWSIC1 results in an overgrowth phenotype when inherited from the father, similar to family A. However, no change in phenotype is observed if the duplication is transmitted through the mother suggesting that increased dosage of maternally expressed genes in the duplicated region has limited effect on the phenotype.

Eye Refraction Anomalies in Down Syndrome Families

Eye Refraction Anomalies in Down Syndrome Families The extra chromosomal material in Down syndrome patients causes a generalised disruption in the genetic balance. From this viewpoint, the non-specific developmental instability following aneuploidy might be also responsible for ocular anomalies in patients with Down syndrome. The aim of this study was to identify the eye refraction anomalies in families having individuals with Down syndrome. A total of 199 Down syndrome patients (average age 17.0 years), 85 their siblings (17.0 years) and 229 their parents (average age 48.9 years) underwent eye refraction examination. In Down syndrome patients ocular refractive findings as spherical equivalent were: emetropia 4.2±1.0%, hypermetropia 70.0±2.3%, and myopia 25.8±2.2%. Astigmatism was diagnosed in 42.8±1.5% of patients. Refraction could not be identified in 3.8±1.0% of patients. In the control group of siblings refractive findings as spherical equivalent were: emmetropia 51.2±3.8%, hypermetropia 39.4±3.7%, and myopia 9.4±2.2%. Astigmatism was diagnosed in 7.6±2.0% of siblings. In parents refractive findings as spherical equivalent were: emmetropia 42.8±2.3%, hypermetropia 40.2±2.3%, and myopia 17±1.8%. Astigmatism was diagnosed in 7.9±1.3% of parents. Refraction could not be identified in 1.1±0.5% of parents. Astigmatism, which is phylogenetically more recent, was found in Down syndrome patients 5.6 times more often than control siblings and 5.4 times more than in the parents group.

De novo 13q partial duplication identified by cytogenetic, biochemical and molecular approaches

A 3.5-month-old female infant manifesting dysmorphic facies, developmental delay and failure to thrive was referred for cytogenetic evaluation. Peripheral lymphocytes revealed three chromosomally distinct cell lines: 46,XX/46,XX,10p+/47,XX,10p+,+mar. Dermal fibroblasts revealed only the 46,XX,10p+cell line. High resolution G-, R-, and Q-banding suggested that the extra chromosomal material (10p+) represented a duplication of the segment 13q14----13qter. Parental karyotypes were normal. As absolute identification of de novo chromosomal abnormalities, based solely on cytogenetic studies, is sometimes difficult, both biochemical and molecular approaches were undertaken to elucidate this abnormality in more detail. Dosage effects were examined using esterase D (localized to 13q14.1) and the DNA probes p1E8 and p9A7 (localized to 13q22 and 13q31/32, respectively). These studies suggested the presence of only 2 copies of esterase D, but 3 copies of both DNA probes, allowing identification of the breakpoint at 13q14.2.

Will resistance in fungi emerge on a scale similar to that seen in bacteria?

Growing numbers of patients receive azoles as prophylaxis or treatment for invasive fungal infections, begging the question of whether emergence of resistance will occur, as has been seen with bacteria. This review examines resistance pathways shared by bacteria and fungi, including alteration and overproduction of drug targets, changes in biosynthetic pathways, and enhanced drug efflux, and assesses whether such commonalities predict increased resistance to azoles. Important differences exist between the two kingdoms, including little, if any, horizontal transfer of extrachromosomal material across fungal species and a longer fungal generation time, thereby slowing vertical transfer of mutant traits. Further, no enzymatic modulation or inactivation of azoles has been reported in fungi. The newer broad-spectrum azoles posaconazole and voriconazole are active against the vast majority of yeasts and moulds and are likely to prevent the emergence of inherently resistant strains. Therefore, the likelihood for an explosion of fungal resistance is relatively low.

Why are some South African children with Down syndrome not being offered cardiac surgery

About 1 in 1,000 children has Down syndrome. Extra chromosomal material results in a myriad of potential problems for the affected individual. About 40% of Down syndrome children will have cardiac abnormalities, ranging from the simple arterial duct to the complex atrioventricular septal defect. Virtually all these defects are amenable to surgical correction and extended survival is possible. In South Africa many of these children do not undergo cardiac surgery.

Prenatal detection of a de novo Yqh-acrocentric translocation

Objectives To identify the extra chromosomal material on 46,XX,21p+ for prenatal diagnosis. Design and methods Conventional cytogenetic studies using GTG (G bands by trypsin using Giemsa) and CBG (C bands by barium hydroxide using Giemsa) techniques were performed on chromosomes at metaphase obtained from cultured amniocytes and parental blood lymphocytes. Molecular cytogenetic techniques, QF-PCR (quantitative fluorescent polymerase chain reaction), FISH (fluorescent in-situ hybridization), and DA-DAPI (Distamycin A and 4,6-diamino-2-phenylindole) staining, were then used to clarify the extra material present on fetal chromosome 21 p. Results The extra material on fetal chromosome 21 p has originated from Yqh, most likely at PAR2 (the secondary pseudoautosomal region). The karyotype should be 46,XX,der(21)t(Y;21)(q12;p13)de novo.ish der(21)t(Y;21)(q12;p13) (EST Cdy16c07+). Conclusion This case demonstrates the usefulness of molecular techniques in the investigation of rare chromosomal rearrangements.