Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2... K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high ¨positive¨ (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller ¨negative¨ (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

Infantile spasm associated with 5q14.3 microdeletion syndrome: clinical and genetic characterization of a core family / 中华儿科杂志

<p><b>OBJECTIVE</b>To characterize the clinical feature of a child with infantile spasm, karyotype and molecular cytogenetic analyses were performed to investigate the cause of disease and choose a suitable prenatal diagnostic method for the couple with the child.</p><p><b>METHOD</b>Routine G-banding was performed to analyze the karyotype of the patient and her parents, and molecular karyotyping was performed using SNP array. Confirmation and segregation studies were performed by fluorescence in situ hybridization (FISH).</p><p><b>RESULT</b>The patient presented with severe psychomotor retardation, epilepsy, muscular hypotonia, stereotypic behavior and facial phenotype characterized by bulging forehead, cupid-bow upper lip, large ears with prominent lobes and pronounced occipital protuberance. Subdural collection of fluid was shown in cranial CT scan, and frequent interictal epileptiform discharges and hypsarrhythmia was shown in EEG monitoring. Routine G-banding revealed a normal female karyotype. A 2.03 Mb deletion in 5q14.3 including MEF2C gene was revealed using SNP array, and the patient's molecular karyotype was arr 5q14.3 (87 538 430-89 565 757) ×1. FISH with locus-specific probe RP11-293L20 from the deleted region on metaphase preparations of the patient and her parents confirmed the de novo occurrence of the deletion.</p><p><b>CONCLUSION</b>The microdeletion of 5q14.3 was the cause of infantile spasm in the patient. FISH confirmed the de novo occurrence of the microdeletion. SNP array should be chosen as prenatal diagnostic method for the couple with the child.</p>

Trisomía 13 y sus alteraciones placentarias. Reporte de caso / Trisomy 13 and its Placental Alterations. Case Report

Las alteraciones cromosómicas son una importante causa de muerte en humanos. Sudiagnóstico cuenta con nuevas herramientas que están cada vez más al alcance y permitencorrelacionar los hallazgos de los estudios fetales y placentarios; sin embargo, no entodas las instituciones de salud colombianas se cuenta con tales recursos. Se reportaun caso de trisomía 13, corroborada por hibridación fluorescente in situ (FISH) y seanalizan las manifestaciones histológicas encontradas en la placenta, la cual sí puedeser estudiada de manera rutinaria...

Chromosome alterations are a major cause of death in humans; diagnosis is now aided bynew technology which allows for cross checking on fetal and placental studies. Althoughmany Colombian medical institutions have inadequate access to this technology, weare able to report on a case of Trisomy 13 in which diagnosis was carried out withFluorescence in situ hybridization (FISH) and the histologic manifestations of theplacenta were analyzed following routine procedures...

Sperm chromatin structure assay predicts the outcome of intrauterine insemination / 中华男科学杂志

<p><b>OBJECTIVE</b>Sperm chromatin structure assay (SCSA), as a clinically practical technique for the analysis of DNA damage, is rarely reported in China. This study focuses on the correlation of DNA damage with the pregnancy rate of intrauterine insemination (IUI).</p><p><b>METHODS</b>We performed semen analysis for 482 couples undergoing IUI, calculated the DNA fragmentation index (DFI) by SCSA, and observed the relationship between DFI and the pregnancy rate of IUI.</p><p><b>RESULTS</b>Clinical pregnancy was achieved in 5 (5.26%) of the 95 cases with DFI > 25%, and in 59 (15.25%) of the 387 cases with DFI < or = 25%. Those with sperm DFI >25% had significantly lower rates of biochemical pregnancy and clinical pregnancy than those with DFI < or = 25% (OR: 0.37, 95% CI: 0.14 - 0.96 and OR: 0.38, 95% CI: 0.16 - 0.97). No significant differences were found in the DFI of 54 cases between the first and the second cycle ([15.05 +/- 7.98]% vs [17.25 +/- 12.18]%, P > 0.05). Sperm DFI was significantly negatively correlated with sperm concentration, sperm motility and total progressively motile sperm count (P < 0.01).</p><p><b>CONCLUSION</b>The pregnancy rate of IUI is significantly lower in couples with DFI >25% than in those with DFI < or = 25%. Sperm DFI obtained from SCSA is partly correlated with sperm concentration and motility, and it is a robust predictor of the IUI outcome.</p>

Estudio citogenético en sangre periférica de pacientes con melanoma / Cytogenetic study in peripheral blood of melanoma patients

En Colombia el melanoma es la principal causa de muerte por enfermedades dermatológicas (40%) y representa el 1% del total de muertes por cáncer. El rápido incremento en la incidencia del melanoma hace necesaria la realización de estudios que permitan entender mejor los mecanismos implicados en su génesis y progresión. En este estudio se determinaron anomalías cromosómicas en sangre periférica de 30 pacientes con melanoma y en 23 individuos control mediante Citogenética Convencional (Bandeo G), observándose alta incidencia de anomalías numéricas y baja incidencia de rearreglos estructurales recurrentes, siendo las pérdidas cromosómicas las alteraciones prevalentes en todos los estadíos tumorales estudiados. El análisis citogenético de los pacientes mostró que, los cromosomas X, 9 y 17 fueron los más frecuentemente afectados. De las anomalías numéricas las monosomías de los cromosomas X y 17 y la trisomía formada por un cromosoma marcador fueron las más frecuentes, en estadíos tempranos y tardíos de la enfermedad. Deleciones y translocaciones se presentaron como anomalías únicas. En el grupo control ningún tipo de anomalía fue identificada, y se observó bajo porcentaje de fragilidades en comparación con el grupo de pacientes. En comparación con los controles se observó alta frecuencia de anomalías cromosómicas en los pacientes, lo que sugiere la existencia de heterogeneidad y predisposición genética en el desarrollo de la enfermedad, que con investigaciones adicionales deben ser analizadas y validadas como posibles fuentes de marcadores moleculares, útiles para el diagnóstico temprano, tratamiento y seguimiento de la enfermedad.

Among all the skin diseases, melanoma is the main cause of death in Colombia (40%) and it represents 1% of all deaths by cancer. Due to the fast increase in the incidence of melanoma, it is necessary to carry out research on the mechanisms involved in its genesis and progression. This study determined chromosomal anomalies from peripheral blood samples on 30 patients with melanoma and on 23 control subjects using conventional cytogenetics (G Banded), where a high incidence in numerical anomalies and a low incidence in recurrent structural rearrangements were observed. Chromosomic losses were prevalent in all the tumor stages studied. The analysis showed that the chromosomes X, 9 and 17 were mainly affected. Among the numerical anomalies, monosomies in X and 17 chromosomes, as well as trisomies formed by a marker chromosome, were the most common in both early and late stages of the disease. Deletions and chromosomal crossovers appeared to be as isolated anomalies. In the control group no anomaly was identified, and a low percentage of fragility was observed when compared with the patients group. A high frequency in chromosomal anomalies was observed in patients, in contrast with the control subjects. This suggests the existence of heterogeneity and genetic predisposition during the illness development. To further research, these must be analyzed and validated as possible sources of molecular markers, which could be of use for the early diagnosis, treatment and follow up of the disease.

Chromosome number and microsporogenesis of two accessions of Brachiaria dura Stapf (Poaceae) / Número de cromossomos e microsporogênese de dois acessos de Brachiaria dura Stapf (Poaceae)

The two accessions of B. dura analyzed (DU01 and DU02) are hexaploid (2n = 6x = 54), derived from x = 9. Meiotic abnormalities, such as precocious chromosome migration to the poles, laggards and micronuclei, were recorded in low frequency in both accessions. The few multivalent chromosome association at diakinesis and meiotic stability suggested that hexaploidy probably resulted from chromosome doubling. In DU02, chromosome transfer (cytomixis) among meiocytes, involving part or the entire genome was observed. The implication of these findings for the Brachiaria breeding is discussed.

Os dois acessos de B. dura analisados (DU01 e DU02) são hexaplóides (2n = 6x = 54), derivados de x = 9. Anormalidades meióticas como migração precoce de cromossomos para os polos, cromossomos retardatários e micronúcleos foram observados em baixa frequência em ambos os acessos. A presença de poucas associações cromossômicas em diacinese e a estabilidade meiótica sugere que a hexaploidia provavelmente resultou de duplicação cromossômica. No acesso DU02 observou-se transferência de cromossomos (citomixia) entre meiócitos, envolvendo parte ou todo o genoma. As implicações destes resultados para o melhoramento de Brachiaria são discutidas.

Chromosome polymorphism in Ancistrus cuiabae Knaack, 1999 (Siluriformes: Loricariidae: Ancistrini)

Cytogenetic and FISH analyses were performed in 30 Ancistrus cuiabae specimens from a bay near the town of Poconé, in the Pantanal of Mato Grosso, Brazil. The observed diploid number was 2n = 34 chromosomes for both sexes and three distinct katyotypic formulae were found, namely cytotype A (20m, 8sm, 6st, Fundamental Number/FN = 68; 6 males and 11 females), cytotype B (19m, 8sm, 6st, 1a, FN = 67; 8 males and 4 females) and cytotype C (18m, 8sm, 6st, 2a, FN = 66; a single male). NORs's analyses showed that these regions were located in distinct sites on the NOR-bearing chromosome pair, according to cytotypes. Thus, in cytotype A, NORs were located in the terminal region of the short arm of the second metacentric chromosome pair; in cytotype B, they were detected in the short arm of the metacentric chromosome and interstitially on the acrocentric chromosome and, in cytotype C, NORs were observed in the interstitial region of the acrocentric chromosome pair. C-positive heterochromatic bands were adjacent to the rDNA sites in the corresponding chromosomes. Thus, the chromosomal polymorphism of A. cuiabae was probably originated through a pericentric inversion in chromosome pair nº 2 involving the NOR sites, which represents a novelty in the Ancistrini tribe. The results also broaden the knowledge of the chromosomal evolution in Ancistrus, the most derived genus of the Ancistrini tribe.(AU)

Foram analisados, com técnicas convencionais de citogenética e FISH, 30 exemplares da espécie Ancistrus cuiabae da baía Arrombado, próximo a Poconé, Pantanal do Mato Grosso. Foram observadas metáfases com número diploide 2n = 34 cromossomos para ambos os sexos e três fórmulas cariotípicas distintas, aqui denominadas de citótipo A, verificado em 06 machos e 11 fêmeas (20m, 8sm, 6st, Número Fundamental, NF = 68); citótipo B, em 08 machos e 04 fêmeas (19m, 8sm, 6st, 1a, NF = 67) e citótipo C em apenas 01 macho (18m, 8sm, 6st, 2a, NF = 66). As NORs confirmaram os distintos citótipos verificados, além de evidenciar que os cromossomos portadores de rDNA são os que representam o polimorfismo na espécie Ancistrus cuiabae. No citótipo A, as NORs foram verificadas na região terminal do braço curto do segundo par de cromossomos metacêntricos; no citótipo B, foram evidenciadas no segundo par, heteromórfico, no braço curto do cromossomo metacêntrico e intersticial no seu homólogo acrocêntrico; no citótipo C as NORs foram observadas na região intersticial num par de cromossomos acrocêntricos. A análise da heterocromatina constitutiva evidenciou blocos discretos adjacentes ao rDNA no segundo par de cromossomos de ambos os citótipos. Uma provável inversão pericêntrica é a hipótese proposta para a origem deste polimorfismo na espécie Ancistrus cuiabae. Estes resultados ampliam o conhecimento sobre o gênero Ancistrus, o mais derivado da tribo, contribuem para o conhecimento sobre este grupo de peixes e para inferir sobre a evolução cromossômica dos Ancistrini(AU)

Detection of subtelomeric rearrangements in patients with idiopathic mental retardation/developmental delay / 中华儿科杂志

<p><b>OBJECTIVE</b>To detect subtelomeric rearrangement in patients with idiopathic mental retardation/developmental delays (MR/DD) and to provide new methods and evidence for the etiologic diagnosis of MR/DD in China.</p><p><b>METHODS</b>1.</p><p><b>INCLUSION CRITERIA</b>(1) Moderate to severe MR/DD; (2) no definite perinatal brain injury; (3) no toxication, hypoxia, infection of central nervous system and cranial trauma; (4) routine karyotyping is normal; (5) no evidence of typical inherited metabolic disorder or specific neurodegenerative disorders from cranial neuro-imaging and blood/urinary metabolic diseases screening; (6) no mutation of FMR1 gene in male patients plus one of the following criteria: (1) positive family history of MR; (2) positive family history of miscarriages and perinatal deaths; (3) abnormal growth; (4) facial and non-facial dysmorphism. 2. Multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) were applied to detect subtelomeric rearrangements in patients and their parents.</p><p><b>RESULTS</b>Four cases were identified from 39 selected cases with subtelomeric rearrangements (10%), including der (2) t (2; 4) (pter; pter), 11qter del, 8pter del, and 15p11.2 del. The first two abnormalities of chromosome subtelomeric regions have not been reported yet. All these cases had some small dysmorphologies, such as microcephaly, hypertelorism, low nasal bridge, and three of them had hypotonia. One case had recurrent seizure and abnormal behavior (laughter not associated with happiness), and another case with dysgenesis of corpus callosum and septum pellucidum. Family and perinatal histories were normal for all cases. All chromosome rearrangements were de novo which were not from the parents with normal phenotype. It indicated that all these abnormal rearrangements should be responsible for the mental retardation phenotype of these patients. The phenotype of case 4 was similar to Angelman syndrome, his deletion was actually a kind of interstitial rearrangements. It will be confirmed by DNA methylation test to determine whether the deleted allele was of maternal origin.</p><p><b>CONCLUSIONS</b>The subtelomeric rearrangements were found in 10% patients with idiopathic MR. It indicated that subtelomeric rearrangements should be one of major reasons of MR/DD related to genetic factors. Two novel subtelomeric rearrangements were identified. These de novo rearrangements are probably disease related, because they are not inherited from their parents with normal phenotype. The detection should be carried out for all the patients with idiopathic MR/DD with unknown origin, because one cannot figure out the specific signs for subtelomeric rearrangements. Sequentially use of MLPA and FISH is a more efficient and economic method to detect the subtelomeric rearrangements.</p>

Estudio de alteraciones cromosómicas y su relación con el crecimiento in vitro en células de meningiomas / Chromosomal alterations of meningioma cells and its relation to growth in vitro

Objetivos: Demostrar la frecuencia de alteraciones cromosómicas y su relación con la velocidad de crecimiento in vitro en cultivos de células de meningiomas. Los datos obtenidos en estudios previos han enseñado que existe una asociación entre las alteraciones cromosómicas con el riesgo de recurrencia y el estadío del tumor. Materiales y métodos: Se sometieron a cultivo muestras tomadas durante la cirugía de resecciones de meningiomas de cualquier localización, en enfermos del HUV, Clínica Rafael Uribe y clínicas particulares, previo consentimiento firmado de los pacientes o familiares. Se realizaron cultivos celulares, se determinó la velocidad de crecimiento y se obtuvo el cariotipo para definir las alteraciones cromosómicas en cada tumor. Resultados: El 47% de los meningiomas que fue posible estudiar, presentan alteraciones cromosómicas diferentes o además de monosomía del cromosoma 22 que según publicaciones previas se asocian con progresión tumoral, y representan un riesgo de recurrencia mayor a 10%. Conclusiones: Los estudios citogenéticos y la velocidad de crecimiento in vitro de las células tumorales, pueden ser un excelente complemento del resultado quirúrgico, del estudio patológico, que contribuirían a establecer el riesgo de recurrencia y así ayudar a definir el pronóstico para el paciente intervenido.

Objectives: To demonstrate the frequency of chromosomic alterations and their relationship to the growth velocity of in vitro meningioma cells cultures. Data obtained in previous studies have shown that there is a kinship between chromosomic alterations, the risk of recurrence and tumor stage. Materials and methods: Samples taken during meningioma resection surgery from any location were cultured. The samples were obtained from patients at the University Hospital, the Rafael Uribe Clinic and private clinics, previous informed consent either from patients or their relatives. Cell cultures were performed, speed of growth was measured, and the karyotype was obtained in order to define the chromosomic alterations present in each tumor. Results: 47% of the meningiomas studied showed different chromosomic alterations or besides monosomy of the chromosome 22 that according to previous publications are associated to tumoral progression and represent a recurrence risk greater than 10%. Conclusions: The cytogenetic studies and the in vitro cellular growth velocity of the tumoral cells could be excellent complements of the surgical result and the pathology study, contributing to establish the risk of recurrence, so helping to define the patient’s prognosis.

Cytogenetic study on 155 cases of non-Hodgkin' s lymphoma / 中华血液学杂志

<p><b>OBJECTIVE</b>To investigate the relationship between histopathological subtype of non-Hodgkin' s lymphoma(NHL) and chromosomal abnormalities, and compare the difference of chromosomal abnormalities between China and the West.</p><p><b>METHODS</b>Routine G banding chromosome analysis and fluorescent in situ hybridization( FISH) were performed on lymph node specimens from 155 NHL patients.</p><p><b>RESULTS</b>Diffuse large B-cell lymphoma( DLBCL) constituted 38.1% of the cases followed by follicular lymphoma(FL) 17.4% , small lymphocytic lymphoma( SLL) 10.3% , peripheral T-cell lymphoma ( PTCL) ( unspecified) 8.4%, and angioimmunoblastic lymphoma 7.1%. One hundred nineteen patients (76. 8%) had clonal chromosomal abnormalities. The incidence of chromosomal abnormalities among FL, SLL, DLBCL, anaplastic large cell lymphoma (ALCL) and precursor T-cell lymphoblastic lymphoma (TLBL) was 96.3% , 87.5% , 86.4%, 83.3% and 83.3%, respectively. Complex karyotype was 86. 3% in DLBCL. The most frequent structural abnormalities in DLBCL involved chromosomes 3, 6, 14 and 1, with had high frequencies of 3q27 (41.2%) and 6q21, 6q23, 6q25 involvement (23.5%). But only 2 cases of DLBCL had classical t( 14; 18) (q32;q21) which was lower than that in the West (20%). The positive rate of IgH rearrangement was 40. 1% in DLBCL by FISH. No 13q14 deletion was found in 16 cases of SLL. Normal karyotype was observed in 8/11 cases with angioimmunoblastic T-cell lymphoma patients.</p><p><b>CONCLUSIONS</b>The distribution of the histopathological subtypes of NHL is different among different geographical areas. The chromosomal abnormalities in DLBCL was comparable between China and the West, but t( 14; 18) was infrequent in the former. The chromosomal abnormalities in SLL was different from the West. The incidence of chromosomal abnormalities in angioimmunoblastic T-cell lymphoma was lower than that in the West.</p>

Progress on the detection techniques for DNA integrity of sperm / 中华男科学杂志

Oxidative stress, deficiencies in natural processes such as chromatin packaging and abortive apoptosis are the main factors that lead to sperm DNA damage. The DNA integrity of sperm is essential for fertilization, as well as for the normal development of the blastocyst, embryo and child. There is increasing evidence that sperm DNA anomalies may lead to infertility, abortion, stillbirth, fathead and chromosomal diseases. The routine examination of semen can not identify subtle defects in sperm DNA, so several detection techniques have been developed for estimating the DNA (nuclear DNA/mitochondria DNA) integrity of sperm, which is considered to be a better marker of male fertility potential than conventional semen parameters. This review attempts at a detailed description of these detection techniques, including their principles, methods, steps and clinical application.

Different Phase of Telomere Shortening with Age in Peripheral Blood Mononuclear Cells / 대한소아혈액종양학회지

PURPOSE: Telomeres, special protein and tandem repeat DNA structure that cap the ends of linear eukaryotic chromosomes, are essential for chromosome structure and stability. Human telomeric DNA is known to shorten by 30~200 bp with each somatic cell division. However, the phase of telomere changes has not been studied extensively. METHODS: Telomere length was analyzed in the peripheral blood mononuclear cells (PBMCs) of 39 normal controls aged from newborn to 72 years by Southern blot hybridization using PharMingen's TeloQunatTM Telomere Length Assay Kit (Becton Dickinson Co.). RESULTS: The mean telomere length of the population was 9.68 kb (range, 5.65~14.40 kb). The length (kb) decreased with age (A) by the following regression: T=10.86 0.04 A (T=telomere length in kb; A=age in years) (r= 0.38; P=0.016). The mean telomere lengths according to age groups were: 10.26 kb for less than 15 years; 9.92 kb for 16 to 40 years; 8.03 kb for over 40 years. The telomere length of over 40 years was significantly shorter than that of less than 15 years (P=0.013), and than that of 16 to 40 years (P=0.011). The phase of telomere changes was evaluated by age subgroups. The shortening was fastest in individuals of age <5, while the length showed a plateau or slight increment in age group between 5 to 35. The length decreased steadily with age by the regression of 12.43+/-0.07 A (r= 0.500; P=0.034) in age group over 35. CONCLUSION: Telomere length of PBMCs decreases with age, and the different phase of telomere length shortening may suggest that the shortening of telomere is not a constant process over lifespan, but a dynamic process that is differently regulated in age groups.

A Cytogenetic Study in Patients with Suspected Y Chromosomal Abnormalities / 대한비뇨기과학회지

A chromosomal study was performed in a tota1 of 98 patients with suspected Y chromosomal abnormalities during past 1-1/2 years (Feb. 1984 -Aug. 1985). Karyotypes were obtained using short-term blood culture. Of these 43 (44%) patients had abnormal chromosome complements. Among all patients with chromosome abnormalities, 88% (38/43) had aberrations of chromosome number and others 32% (5/42) had aberrations of chromosome structure. The results of chromosomal study in various groups showed as follows: l. In 34 cases of Klinefelter's syndrome, there were 31 cases (91%) of 47,XXY, 1 case of 46,XX,47, XXY, 1 case of 48, XXXXY and 1 case of 46,XX/46,XY/47,XXY. 2. AII 3 cases of mixed gonadal dysgenesis had 45,X/46,XY. 3. l case of true hermaphroditism had 46,XX. 4. Z cases of male Turner`s syndrome, 6 cases of male pseudohermaphroditism and 1 case of agonadism had 46,XY. 5. In 6 cases of female pseudohermaphroditism, there were 4 cases of 46,XX, 1 case of 46,XX, inv(9) and 1 case of 46,XX, t (14q, 21q). 6. In 28 cases of hypogonadism (excluding Klinefelter`s syndrome), there were 25 cases (89%) of 46, XY, 1 case of 46,XY, 15s-, 1 case of 46,XY, inv(9) and 1 case of 46,XY/46, XY,t(7 : 14). 7. 1 case of cryptorchism had 47,XY,+21. 8. All of 5 cases of hypospadia, 5 cases of cryptorchism, 3 cases of hypospadia with cryptorchism, 2 cases of small phallus, 1 case of concealed penis and 1 case of normal male who wanted to correct his registered sex had 46,XY.