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Almulhim A, Almoallem B, Alsirrhy E, Osman EA. Unique Roberts syndrome with bilateral congenital glaucoma: A case report. World J Clin Cases 2023; 11:4635-4639. [PMID: 37469722 PMCID: PMC10353501 DOI: 10.12998/wjcc.v11.i19.4635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/19/2023] [Accepted: 04/20/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Congenital glaucoma associated with Roberts syndrome (RS) is an unusual and unique condition. No previous report describes this association. A multidisciplinary approach including molecular studies were conducted to reach the final diagnosis.
CASE SUMMARY We present a rare case of a 1-wk-old male with RS associated with bilateral congenital glaucoma, left ectopic kidney, and left-hand rudimentary digits. A comprehensive approach was applied by which bilateral non-penetrating glaucoma surgery was performed with good control of intraocular pressure for more than 6 mo. Cytogenetic and molecular testing were conducted and revealed normal measurements.
CONCLUSION This report described a case of a male baby with clinical features of RS but with a negative molecular analysis, presenting with left-hand rudimentary digits, bilateral congenital glaucoma, and left ectopic kidney. To the best of our knowledge, this is the first case reported with phocomelia, bilateral congenital glaucoma, and unilateral ectopic kidney.
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Middlebrooks B, McCue P, Nelson B, May E, Divine C, Barton C, Conley A. Monorchidism in a Phenotypic Mare With a 64,XY, SRY-Positive Karyotype. J Equine Vet Sci 2023; 126:104232. [PMID: 36736748 DOI: 10.1016/j.jevs.2023.104232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Disorders of sexual development (DSD) are associated with atypical chromosomal, gonadal, or phenotypic sex. It is likely that the number of cases of DSD are underestimated in the equine population. Monorchidism in the horse is very rare. This case report describes the clinical assessment of a phenotypic mare with stallion-like behavior which led to the diagnosis of a DSD. A 4-year-old Quarter Horse mare presented in good body condition, with normal external genitalia for a mare, and normal mammary glands with two bilaterally symmetric teats. No uterus, cervix, or gonads were detected on transrectal palpation. Transrectal ultrasonography revealed a single gonad in the right dorsal abdomen with the morphologic appearance of a testicle. Presurgical hormonal evaluation revealed elevated serum testosterone and anti-Müllerian hormone (AMH) concentrations. The right gonad was successfully removed via standing exploratory laparoscopy and submitted for histopathology. No gonad was identified on the left side during laparoscopy. Histopathologic examination confirmed that the excised gonad was a testicle. Cytogenetic and molecular analysis revealed a 64,XY, SRY-positive chromosomal constitution. Hormonal evaluation 5 weeks after surgery revealed low serum testosterone and AMH levels. A diagnosis of monorchidism was based on ultrasound examination, laparoscopic exploration of the abdomen, removal of a single gonad, and a subsequent decrease in serum testosterone and AMH concentrations to basal levels. In summary, a combination of clinical signs, endocrine evaluation, chromosomal and molecular analysis, and histopathology can be used in the diagnosis of DSD conditions.
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Zhou M, Lu Y, Han L, Lu M, Guan C, Yu J, Liu H, Chen D, Li H, Yang Y, Zhang L, Tian L, Liu Q, Hou Z. Exploration of Parascaris species in three different Equus populations in China. Parasit Vectors 2023; 16:202. [PMID: 37322493 DOI: 10.1186/s13071-023-05768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/04/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND The roundworms, Parascaris spp., are important nematode parasites of foals and were historically model organisms in the field of cell biology, leading to many important discoveries. According to karyotype, ascarids in Equus are commonly divided into Parascaris univalens (2n = 2) and Parascaris equorum (2n = 4). METHODS Here, we performed morphological identification, karyotyping and sequencing of roundworms from three different hosts (horses, zebras and donkeys). Phylogenetic analysis was performed to study the divergence of these ascarids based on cytochrome c oxidase subunit I (COI) and internal transcribed spacer (ITS) sequences. RESULTS Karyotyping, performed on eggs recovered from worms of three different Equus hosts in China, showed two different karyotypes (2n = 2 in P. univalens collected from horses and zebras; 2n = 6 in Parascaris sp. collected from donkeys). There are some differences in the terminal part of the spicula between P. univalens (concave) and Parascaris sp. (rounded). Additionally, it was found that the egg's chitinous layer was significantly thicker in Parascaris sp. (> 5 μm) than P. univalens (< 5 μm) (F(2537) = 1967, P < 0.01). Phylogenetic trees showed that the sequences of Parascaris from Equus hosts were divided into two distinct lineages based on sequences of the COI and ITS. CONCLUSIONS Comparing the differences in roundworms collected from three different Equus hosts, this study describes a Parascaris species (Parascaris sp.) with six chromosomes in donkeys. It is worth noting that the thickness of the chitinous layer in the Parascaris egg may serve as a diagnostic indicator to distinguish the two roundworms (P. univalens and Parascaris sp.). The Parascaris sp. with six chromosomes in donkeys in the present study may be a species of P. trivalens described in 1934, but the possibility that it is a new Parascaris species cannot be ruled out. Both karyotyping and molecular analysis are necessary to solve the taxonomic problems in Parascaris species.
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Song M, Zhang T, Yang D, Xiao H, Wang H, Ye Q, Zhai Z. Chromosomal aberrations and prognostic analysis of secondary acute myeloid leukemia-a retrospective study. PeerJ 2023; 11:e15333. [PMID: 37214104 PMCID: PMC10194067 DOI: 10.7717/peerj.15333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Background Secondary acute myeloid leukemia (S-AML) patients generally have a poor prognosis, but the chromosomal aberrations of S-AML have been rarely reported. We aimed to explore the chromosomal aberrations and clinical significance in patients with S-AML. Patients and methods The clinical characteristics and karyotypes of 26 patients with S-AML were retrospectively analyzed. The overall survival (OS) was measured from the time of the patients' transition to AML (i.e., at S-AML diagnosis). Results The study included 26 S-AML patients (13 males and 13 females), with a median age of 63 years (range, 20-77 years). They transformed from various hematologic malignancies or solid tumors; most of them were secondary to myelodysplastic syndrome (MDS). About 62% of the S-AML patients showed chromosomal aberrations. The serum lactate dehydrogenase (LDH) level in S-AML patients with abnormal karyotype was higher than those with normal karyotype. Apart from the differences in treatment regimens, S-AML patients with chromosomal aberrations had shorter OS (P < 0.05). Conclusion S-AML patients with abnormal karyotype have higher LDH levels and shorter OS than normal karyotype patients, and the OS of hypodiploidy was much shorter than hyperdiploid.
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de Andrade ARM, Cardoso DC, Cristiano MP. Assessing ploidy levels and karyotype structure of the fire ant Solenopsissaevissima Smith, 1855 (Hymenoptera, Formicidae, Myrmicinae). COMPARATIVE CYTOGENETICS 2023; 17:59-73. [PMID: 38059050 PMCID: PMC10696605 DOI: 10.3897/compcytogen.17.100945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/07/2023] [Indexed: 12/08/2023]
Abstract
The family Formicidae is composed of ants that organize themselves into castes in which every individual has a joint organizational function. Solenopsis Westwood, 1840 is an ant genus with opportunistic and aggressive characteristics, known for being invasive species and stings that cause burning in humans. This genus is particularly difficult to classify and identify since its morphology provides few indications for species differentiation. For this, a tool that has been useful for evolutionary and taxonomic studies is cytogenetics. Here, we cytogenetically studied Solenopsissaevissima Smith, 1855 from Ouro Preto, Minas Gerais, Brazil. We evaluated the occurrence of polyploid cells in individuals and colonies by conventional cytogenetics. A total of 450 metaphases were analyzed and counted. Chromosome counts of individuals and colonies showed varied numbers of ploidies, from n = 16 to 8n = 128. The karyomorphometrical approach allowed determination of the following karyotypes: n = 10 m + 4 sm + 2 st, 2n = 20 m + 8 sm + 4 st, and 4n = 40 m + 16 sm + 8 st. Polyploidy can be found naturally in individuals and colonies and may represent an adaptative trait related to widespread distribution and invasion ability of new habitats.
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Součková K, Jasík M, Sovadinová I, Sember A, Sychrová E, Konieczna A, Bystrý V, Dyková I, Blažek R, Lukšíková K, Pavlica T, Jankásek M, Altmanová M, Žák J, Zbončáková A, Reichard M, Slabý O. From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106517. [PMID: 37087860 DOI: 10.1016/j.aquatox.2023.106517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
There is a growing need of alternative experimental models that avoid or minimize the use of animals due to ethical, economical, and scientific reasons. Surprisingly, the stable embryonic cell lines representing Nothobranchius spp., emerging vertebrate models in aging research, regenerative medicine, ecotoxicology, or genomics, have been not derived so far. This paper reports establishment and deep characterization of ten continuous cell lines from annual killifish embryos of N. furzeri and N. kadleci. The established cell lines exhibited mostly fibroblast- and epithelial-like morphology and steady growth rates with cell doubling time ranging from 27 to 40 h. All cell lines retained very similar characteristics even after continuous subcultivation (more than 100 passages) and extended storage in liquid nitrogen (∼3 years). The cytogenetic analysis of the cell lines revealed a diploid chromosome number mostly equal to 38 elements (i.e., the native chromosome count for both killifish species), with minor but diverse line/passage-specific karyotype changes compared to the patterns observed in non-cultured N. furzeri and N. kadleci somatic cells. Based on transcriptional analysis of marker genes, the cell lines displayed features of an undifferentiated state without signs of senescence even in advanced passages. We confirmed that the cell lines are transfectable and can form viable 3-D spheroids. The applicability of the cell lines for (eco)toxicological surveys was confirmed by assessing the effect of cytotoxic and growth inhibitory agents. Properties of established Nothobranchius embryonic cell lines open new possibilities for the application of this model in various fields of life sciences including molecular mechanisms of aging, karyotype (in)stability or differences in lifespan.
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Poisson W, Prunier J, Carrier A, Gilbert I, Mastromonaco G, Albert V, Taillon J, Bourret V, Droit A, Côté SD, Robert C. Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 2023; 24:142. [PMID: 36959567 PMCID: PMC10037892 DOI: 10.1186/s12864-023-09189-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. RESULTS We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.
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Integrated genetic profiling of archival pediatric high-grade glial tumors and reassessment with 2021 WHO classification of paediatric CNS tumours. Cancer Genet 2023; 274-275:10-20. [PMID: 36917897 DOI: 10.1016/j.cancergen.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Though rare, pediatric high-grade gliomas (pHGG) are a leading cause of cancer-related mortality in children. We wanted to determine whether our currently available clinical laboratory methods could better define diagnosis for pHGG that had been archived at our institution for the past 20 years (1998 to 2017). We investigated 33 formalin-fixed paraffin-embedded pHGG using ThermoFisher Oncoscan SNP microarray with somatic mutation analysis, Sanger sequencing, and whole genome sequencing. These data were correlated with historical histopathological, chromosomal, clinical, and radiological data. Tumors were subsequently classified according to the 2021 WHO Classification of Paediatric CNS Tumours. All 33 tumors were found to have genetic aberrations that placed them within a 2021 WHO subtype and/or provided prognostic information; 6 tumors were upgraded from WHO CNS grade 3 to grade 4. New pHGG genetic features were found including two small cell glioblastomas with H3 G34 mutations not previously described; one tumor with STRN-NTRK2 fusion; and a congenital diffuse leptomeningeal glioneuronal tumor without a chromosomal 1p deletion but with KIAA1549-BRAF fusion. Overall, the combination of laboratory methods yielded key information for tumor classification. Thus, even small studies of these uncommon tumor types may yield new genetic features and possible new subtypes that warrant future investigations.
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Teixeira GA, Jacintho GDF, de Aguiar HJAC, Lopes DM, Barros LAC. Cytogenetic Analysis of the Fungus-Farming Ant Cyphomyrmex rimosus (Spinola, 1851) (Formicidae: Myrmicinae: Attini) Highlights Karyotypic Variation. Cytogenet Genome Res 2023; 162:579-586. [PMID: 36848876 DOI: 10.1159/000529607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
The fungus-farming ant genus Cyphomyrmex (subtribe Attina, clade Neoattina) comprises 23 described species that are widely distributed throughout the Neotropics. Species within Cyphomyrmex have taxonomic issues such as Cyphomyrmex rimosus (Spinola, 1851) which is likely a species complex. Cytogenetics is a useful tool for evolutionary studies and understanding species with dubious taxonomy. In this study, we characterized the karyotype of C. rimosus from Viçosa, Minas Gerais State, southeastern Brazil using classical and molecular cytogenetic techniques to enrich the chromosomal information about Cyphomyrmex. The karyotype of C. rimosus from the rainforest of southeastern Brazil (2n = 22, 18m + 4sm) notably contrasts with that previously described for this species in Panama (2n = 32). This intraspecific chromosomal variation suggests the existence of a species complex within this taxon according to the previous hypothesis derived from morphological analysis. We detected GC-rich heterochromatic regions in C. rimosus and, using repetitive DNA probes, showed that this heterochromatin shares repetitive sequences with other Neoattina species already studied, enhancing the importance of this specific genome region in the understanding of Attina evolution. Mapping of microsatellite (GA)15 on C. rimosus was restricted to the euchromatic regions of all chromosomes. The single intrachromosomal rDNA sites observed in C. rimosus follow the general genomic organization trend of ribosomal genes in Formicidae. Our study extends the data of chromosome mapping on Cyphomyrmex and reinforces the importance of cytogenetic studies in different localities to better understand taxonomic issues in widely distributed taxa such as C. rimosus.
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Zhou Y, Wu S, Han J, Zhen L, Yang X, Li R, Zhang Y, Jing X, Li F, Liu H. Prenatal diagnosis of ultrasound soft markers in a single medical center of mainland China. Mol Cytogenet 2023; 16:3. [PMID: 36765363 PMCID: PMC9912520 DOI: 10.1186/s13039-022-00633-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/20/2022] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND There are a few studies on the chromosomal aberration of Ultrasound soft markers (USMs). The aim of this study was to determine the detection rate of clinically significant chromosomal abnormalities (CSCA) in fetuses with different USMs. METHODS This study included fetuses with USMs who underwent invasive prenatal diagnosis for karyotype and/or chromosomal microarray (CMA) by categorizing into two groups: a single USM (SUSM) and multiple USMs (MUSMs). RESULTS Of the 358 cases with USMs, CSCA occurred in 3.09% (8/259) and 8.08% (8/99) of the SUSM and MUSM groups, respectively (P < 0.05). Of 16 cases identified with CSCA, theoretically 68.75% (11/16) could be detected by karyotype, while 31.25% (5/16) could be recognized only by CMA. Among CSCA cases, the most frequent USM was an absent or hypoplastic nasal bone (62.5%, 10/16). In cases with negative karyotypes and/or CMA, follow-up results were available in 307 cases, including 292 term deliveries, 6 preterm deliveries, 8 terminations of pregnancy due to USMs, and 1 still birth. CONCLUSION MUSMs increased the risk of chromosomal abnormalities. An absent or hypoplastic nasal bone was the most clinically significant marker either alone or in combination with other USMs. Most of SUSM had a good prognosis.
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Array study in fetuses with nuchal translucency above the 95th percentile: a 4-year observational single-centre study. Arch Gynecol Obstet 2023; 307:285-292. [PMID: 35486155 DOI: 10.1007/s00404-022-06564-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/05/2022] [Indexed: 02/02/2023]
Abstract
PURPOSE To evaluate the performance of chromosomal microarray analysis (CMA) in fetuses with nuchal translucency (NT) > 95th percentile. Secondary objectives were to analyze these results according to NT thickness, below or above 3.5 mm, and those without associated anomalies. METHODS This observational single-cohort study was conducted between 2015 and 2018 in fetuses with NT > 95th percentile. Following an invasive test, quantitative fluorescence-polymerase chain reaction (QF-PCR) was performed, and if normal, CMA was performed. Pathogenic copy number variants (CNVs), non-reported pathogenic CNV, pathogenic autosomal recessive variants and variants of unknown significance (VUS) were analysed. RESULTS One-hundred and sixty-two fetuses with NT > 95th percentile, normal QF-PCR and CMA were included. Amongst 128 fetuses with NT between the 95th percentile and 3.5 mm, one (0.8%) had a pathogenic CNV, four (3.1%) had non-reported pathogenic CNV, one (0.8%) had pathogenic autosomal recessive variant and 13 (10.2%) had VUS. Amongst 34 fetuses with NT ≥ 3.5 mm, four (11.8%) had pathogenic CNV, one (2.9%) had non-reported pathogenic CNV, one (2.9%) had pathogenic autosomal recessive variant and four (11.8%) had VUS. Four in 162 (2.5%) fetuses had CNVs at the chromosome 16p13.11 region. Amongst 154 fetuses without structural abnormalities and normal QF-PCR, three (1.9%) had a pathogenic CNV, 5 (3.2%) had non-reported pathogenic CNV, one (0.6%) autosomal recessive pathogenic CNV and 16 (10.4%) had VUS. CONCLUSION Pathogenic CNVs were found in 1% of fetuses with an NT thickness between the 95th percentile and 3.5 mm and in 12% of fetuses with NT ≥ 3.5 mm. CNVs were found at the 16p13.11 region in 2.5% of cases.
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Rodríguez-González R, Gutiérrez ML, Fuentes I, Gálvez-Prada F, Sochorová J, Kovařík A, Garcia S. Release 4.0 of the Plant rDNA Database: A Database on Plant Ribosomal DNA Loci Number, Their Position, and Organization: An Information Source for Comparative Cytogenetics. Methods Mol Biol 2023; 2703:237-245. [PMID: 37646950 DOI: 10.1007/978-1-0716-3389-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This paper presents the latest update to the Plant rDNA database (Release 4.0), a valuable resource for researchers in the field of plant cytogenetics. The database provides information on the number, position, and arrangement of ribosomal DNA loci in plants, including angiosperms, gymnosperms, bryophytes, and pteridophytes. The new release includes new data for 820 species coming from additional 173 papers. In the updated version of the Plant rDNA database, 4948 entries comprising 2760 organisms can be found. A brief guide on how to navigate the database and obtain the desired information is also provided. The regular updating of the database is important for ensuring the information it contains is accurate, up-to-date, and useful for the research community. The Plant rDNA database continues to be beneficial for phylogenetic and cytogenetic studies in a wide range of taxa including angiosperms, gymnosperms, and early diverging groups, such as bryophytes and lycophytes.
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Kalantari H, Sabbaghian M, Vogiatzi P, Rambhatla A, Agarwal A, Colpi GM, Sadighi Gilani MA. Bridging the Gap between AZF Microdeletions and Karyotype: Twelve Years' Experience of an Infertility Center. World J Mens Health 2023:41.e7. [PMID: 36593709 DOI: 10.5534/wjmh.220089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Despite all past efforts, the current guidelines are not explicit enough regarding the indications for performing azoospermia factor (AZF) screening and karyotype, burdening clinicians with the decision to assess whether such tests are meaningful for the infertile male patient. These assessments can be costly and it is up to the healthcare practitioner to decide which are necessary and to weigh the benefits against economic/psychological harm. The aim of this study is to address such gaps and provide update on current management options for this group of patients. MATERIALS AND METHODS To address such gaps in male infertility management and to elucidate whether AZF screening is indicated in individuals who concomitantly harbor chromosomal abnormalities we conducted a retrospective cohort analysis of 10,388 consecutive patients with non-obstructive azoospermia (NOA) and severe oligozoospermia. RESULTS Previously, it has been suggested that all NOA cases with chromosomal defects, except males with 46,XY/45,X karyotype, have no indication for AZF screening. Our findings revealed that cases carrying the following chromosomal abnormalities inv(Y)(p11.2q12); idic(Y)(q11.2); 46,XY,r(Y); idic(Y)(p11.2) and der(Y;Autosome) (76/169; 44.9%; 95% CI, 37.7-52.5) should also be referred for AZF deletion screening. Here, we also report the correlation between sperm count and AZF deletions as a secondary outcome. In accordance with previously reported data from North America and Europe, our data revealed that only 1% of cases with >1×106 sperm/mL had Y chromosome microdeletions (YCMs). CONCLUSIONS In the era of assisted reproduction, finding cost-minimization strategies in infertility clinics without affecting the quality of diagnosis is becoming one of the top prioritized topics for future research. From a diagnostic viewpoint, the results reflect a need to reconsider the different karyotype presentations and the sperm count thresholds in male infertility guidelines as indicators for YCM screening during an infertility evaluation.
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Sader MA, Costa LA, Souza G, Urdampilleta JD, Simon J, Vaio M. South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent. Methods Mol Biol 2023; 2703:211-225. [PMID: 37646948 DOI: 10.1007/978-1-0716-3389-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Chromosome numbers have been used in plant taxonomy, and they are still fundamental for taxon delimitation and genome evolution studies. South America is one of the most diverse continents in terms of plant species and there is a considerable number of species not yet analyzed. Accumulated knowledge about plant chromosome numbers has been compiled from online databases, and here we present an overview. The CCDB is one of the largest plant cytological databases and includes data for around 18% of known vascular plants in the world. In this work, we review the information contained in CCDB and in three databases with exclusive information for South America. At present, the three existing databases comprise information on around 1800 plant taxa related to specific regions, countries, or biomes. Efforts are necessary to expand cytological knowledge and to collect all the available information in a plant chromosome database for this continent.
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Gutiérrez ML, Rodríguez-González R, Fuentes I, Gálvez-Prada F, Kovařík A, Garcia S. First Update to B-Chrom: A Database on B-Chromosomes. Methods Mol Biol 2023; 2703:227-236. [PMID: 37646949 DOI: 10.1007/978-1-0716-3389-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The supernumerary mostly dispensable B chromosomes are nuclear components of about 15% of eukaryotic phyla. For a long time, B chromosomes have been studied, generating an enormous bulk of knowledge, diluted in the vastness of the scientific literature. In order to provide better access to this information, we created B-chrom ( www.bchrom.csic.es ), an online database with comprehensive information on Bs for plants, animals, and fungi. It was released in 2017 and first updated in 2021, by adding 334 entries and 123 new species. Currently, the resource provides information for 2951 species coming from 3292 sources. During this time, the usefulness of this database has been proven by the number of visits (more than 207,000 since its release) and by the scientific community, having been cited in more than 60 publications until present. This chapter explains the database composition and tips on how to use it.
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Gutiérrez ML, Rodríguez-González R, Pascual-Díaz JP, Fuentes I, Garcia S. Online Resources Useful for Plant Cytogenetics and Cytogenomics Research. Methods Mol Biol 2023; 2672:549-560. [PMID: 37335499 DOI: 10.1007/978-1-0716-3226-0_33] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The advancements in research in the field of plant cytogenetics and genomics in recent decades have led to a significant increase in publications. To simplify access to the widely dispersed data, there has been a rise in the number of online databases, repositories, and analytical tools. This chapter presents a comprehensive overview of these resources, which can be beneficial to researchers in these areas. It includes, among others, databases on chromosome numbers, special chromosomes (such as B chromosomes or sex chromosomes), some of which are taxon-specific; genome sizes, cytogenetics; and online applications and tools for genomic analysis and visualization.
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Harfsheno M, Barati M, Roohandeh A. First Trimester Screening Tests Pregnancy and Trisomy 13 Syndrome, Sex Chromosome Aneuploidy in Iran: A Cross-Sectional Study. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2023; 17:34-39. [PMID: 36617200 PMCID: PMC9807894 DOI: 10.22074/ijfs.2022.542511.1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Trisomy 13 (T13) and sex chromosome aneuploidies (SCA) are the vital causes of congenital malformations. This study was performed to identify the T13 and SCA with screening tests in the first trimester of pregnancy. MATERIALS AND METHODS In this cross-sectional study, first-trimester combined screening was conducted on 2100 pregnant women referred to Narges Genetics Laboratory, Ahvaz, Iran. Evaluating the first trimester screening tests, including nuchal translucency (NT), crown-rump length (CRL) and pregnancy-associated plasma protein-A (PAPP-A), and free beta of human chorionic gonadotropin (fβhCG) was performed. For a definitive diagnosis of T13 and SCA syndrome, fetal karyotype was evaluated. RESULTS The average NT and CRL in high-risk group for T13 were 5.96 mm and 61.7 mm respectively and in high-risk groups for SCA were 3.7 mm and 75.9 mm, respectively. Significant correlation was observed among NT, CRL and T13, SCA (P<0.05). The average serum fβhCG and PAAP-A levels in high-risk group for T13 were 0.42 and 0.31, respectively. Significant correlation was observed between decrease fβhCG, PAPP-A and T13 levels and increase fβhCG levels and SCA levels (P<0.05). No Significant correlation was observed between PAPP-A levels and SCA levels (P>0.05). CONCLUSION Using special software and karyotype testing, the prenatal screening tests based on the maternal age and gestational age in the first trimester of pregnancy may determine the major risk of fetal chromosomal abnormalities.
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Schwarzacher T, Liu Q, Pat Heslop-Harrison JS. Plant Cytogenetics: From Chromosomes to Cytogenomics. Methods Mol Biol 2023; 2672:3-21. [PMID: 37335467 DOI: 10.1007/978-1-0716-3226-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical development of preparation methods, microscopes, and chemicals to stain them, with latest continuing developments described in this volume. At the end of the twentieth and beginning of the twenty-first centuries, DNA technology, genome sequencing, and bioinformatics have revolutionized how we see, use, and analyze chromosomes. The advent of in situ hybridization has shaped our understanding of genome organization and behavior by linking molecular sequence information with the physical location along chromosomes and genomes. Microscopy is the best technique to accurately determine chromosome number. Many features of chromosomes in interphase nuclei or pairing and disjunction at meiosis, involving physical movement of chromosomes, can only be studied by microscopy. In situ hybridization is the method of choice to characterize the abundance and chromosomal distribution of repetitive sequences that make up the majority of most plant genomes. These most variable components of a genome are found to be species- and occasionally chromosome-specific and give information about evolution and phylogeny. Multicolor fluorescence hybridization and large pools of BAC or synthetic probes can paint chromosomes and we can follow them through evolution involving hybridization, polyploidization, and rearrangements, important at a time when structural variations in the genome are being increasingly recognized. This volume discusses many of the most recent developments in the field of plant cytogenetics and gives carefully compiled protocols and useful resources.
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Yücel G, Senderowicz M, Kolano B. The Use of Ribosomal DNA for Comparative Cytogenetics. Methods Mol Biol 2023; 2672:265-284. [PMID: 37335483 DOI: 10.1007/978-1-0716-3226-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.
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Jara-Seguel P, Urrutia-Estrada J. Chilean Plants Cytogenetic Database: An Online Resource for Embryophytes of the Southern Cone. Methods Mol Biol 2023; 2703:193-200. [PMID: 37646946 DOI: 10.1007/978-1-0716-3389-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Chilean Plants Cytogenetic Database (CPCD) is a resource available online in electronic format, providing a cytogenetics catalog for continental and insular Chilean plants that are representative of the floras of the Southern Cone. In the last update carried out in 2021, we increased the cytogenetic data for 499 Chilean native species, and from here on we will include a new section with chromosome number data for 683 exotic species classified as invaders in Chile. Aspects on the coverage, features, and uses of the CPCD are presented here, including background information accumulated since its inception in 2010 to the present. With the new update, the database currently stores cytogenetic information for species belonging to the divisions Bryophyta, Pteridophyta, Pinophyta, and Magnoliophyta, thus contributing to the largest community resource on plant cytogenetics in the world.
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Zhang M, Zhao Y, Wang L, Zheng Y, Yu H, Dong X, He W, Yin Z, Wang Z. Study of the biological characteristics of human umbilical cord mesenchymal stem cells after long-time cryopreservation. Cell Tissue Bank 2022; 23:739-752. [PMID: 35066739 PMCID: PMC9675661 DOI: 10.1007/s10561-021-09973-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023]
Abstract
Human umbilical cord mesenchymal stem cells (hUC-MSCs) have considerable potential in cell therapy. Cryopreservation represents the gold standard in cell storage, but its effect on hUC-MSCs is still not well understood. The aim of this study was to investigate the effect of one year of cryopreservation and thawing on the biological characteristics of hUC-MSCs from the same donors. Fresh hUC-MSCs were cryopreserved in commercial freezing medium (serum-free CellBanker 2) at passage 2. After one year of cryopreservation, the hUC-MSCs were thawed and subcultured to passage 4. The comparison was performed in terms of followings: cell count, viability, morphology, proliferation capacity, differentiation potential and chromosomal stability. The total cell count and viability of hUC-MSCs before and after one year of cryopreservation were 1 × 107 and 96.34% and 0.943 × 107 and 93.81%, respectively. Cryopreserved and fresh hUC-MSCs displayed a similar cell doubling times, expressed the markers CD73, CD90, CD105 and were negative for the markers CD34, CD45, and HLA-DR. Karyotypes were found to be normal after one year of cryopreservation. The trilineage differentiation properties were maintained after cryopreservation. However, when compared to freshly isolated hUC-MSCs from the same donor, cryopreserved hUC-MSCs exhibited decreased expression of osteogenesis- and chondrogenesis-related genes including Runx2, Sox9, and Col1a1, and increased expression of adipogenesis-related genes. These results demonstrated that cryopreservation did not affect cell morphology, surface marker expression, cell viability, proliferative capacity, or chromosomal stability. However, the osteogenic and chondrogenic differentiation capacities of cryopreserved hUC-MSCs were slightly reduced compared with those of fresh cells from the same donor.
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Pande S, Babu S, Gawde H. Exome Sequencing, whom to Test? A Case Report of Rare Genetic Findings in Consanguineous Couple with Two Neonatal Deaths. J Obstet Gynaecol India 2022; 72:409-411. [PMID: 36457441 PMCID: PMC9701273 DOI: 10.1007/s13224-022-01715-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/14/2022] [Indexed: 10/14/2022] Open
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Pavlicek J, Soucek O, Vrtel R, Klaskova E, Hana V, Stara V, Adamova K, Fürst T, Hana V, Kapralova S, Prochazka M, Snajderova M, Tomaskova H, Tüdös Z, Vrbicka D, Vrtel P, Zapletalova J, Tauber Z, Lebl J. Karyotyping of Lymphocytes and Epithelial Cells of Distinct Embryonic Origin Does Not Help to Predict the Turner Syndrome Features. Horm Res Paediatr 2022; 95:465-475. [PMID: 35970147 DOI: 10.1159/000525823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/08/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In Turner syndrome (TS), fluorescent in situ hybridization (FISH) karyotyping offers an alternative to classical karyotyping. OBJECTIVE We tested the added value of FISH karyotyping from lymphocytes (mesodermal origin), buccal cells (ectodermal origin), and a rear-tongue smear (endodermal origin) to determine the 45,X cell line fraction and its impact on patient phenotype. DESIGN AND PATIENTS Classical karyotyping and three FISH assays were done in 153 girls and women previously diagnosed with TS in four university hospitals. The 45,X cell line fraction was determined for each method and correlated with the major phenotypic signs. RESULTS Classical karyotyping identified 45,X/46,XX mosaicism in 77/153 subjects (50%), 45,X monosomy in 52/153 (34%), and other karyotypes in 24/153 (16%). FISH from lymphocytes verified 45,X in 47/52 original cases, whereas 4/52 had 45,X/46,XX and 1/52 45,X/47,XYY mosaicism. The 45,X cell line fraction was higher in FISH from lymphocytes compared to classical karyotyping (median 86.4% vs. 70.0%; p < 0.001), while there was no difference for FISH from buccal or rear-tongue smear cells. The mean 45,X cell line fraction was more abundant in patients with several of the characteristic phenotypic signs compared to patients without them (p < 0.01), but the predictive power was insufficient. CONCLUSION FISH analysis confirmed the findings of classical karyotyping; only a few 45,X monosomy cases were reclassified as mosaics. The 45,X cell line fraction did not show clinically meaningful prediction of the phenotype. FISH analysis of buccal or rear-tongue epithelial cells may be a non-inferior, less invasive alternative to classical karyotyping.
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Meena JP, Pathak N, Gupta AK, Bakhshi S, Gupta R, Makkar H, Seth R. Molecular evaluation of gene mutation profiles and copy number variations in pediatric acute myeloid leukemia. Leuk Res 2022; 122:106954. [PMID: 36162216 DOI: 10.1016/j.leukres.2022.106954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND The objectives of this study were to investigate the mutation profiles of targeted genes and copy number variations (CNVs) in normal cytogenetics (CN) pediatric acute myeloid leukemia (AML). METHODS This prospective study was conducted from October 2018 to December 2020. The next-generation sequencing (NGS) and chromosomal microarray analyses (CMA) were performed in pediatric CN-AML patients. RESULTS Out of 94 children (aged ≤18 years), 70 patients with AML (24 excluded) underwent conventional karyotyping/cytogenetic analyses. Forty-five (64.3%) of patients had abnormal/ recurrent cytogenetic abnormalities and 25 (35.7%) had normal cytogenetics. Twenty-three out of 25 CN-AML were further processed for gene mutation profile and CNVs using NGS and CMA, respectively. Twenty-two out of 23 (95.7%) patients were detected to have mutations in various genes. The common mutations were: NRAS, NPM1, CEBPA, KRAS, KIT, RUNX1, NOTCH1, WT1, GATA1, GATA2, FLT3, KMT2D, FLT3-TKD, and PHF6. Copy number variations (CNVs) were detected in nine patients (39%), and eight (34.8%) had a long contiguous stretch of homozygosity (LCSH) /loss of heterozygosity (LOH). An LCSH was detected on chromosomes 5, 7, 11, and 19. The gains were more common than losses (8 vs 2). The gains were observed on chromosomes 8, 9, 14, 19, 21, and 22, and the losses were detected on chromosomes 7 and 10. Monosomy was observed in three patients. Three patients (monosomy7, n = 2, and FLT-ITD, n = 1) were reclassified into the high-risk category. Post-induction, complete remission was achieved in all evaluable patients. CONCLUSION CN-AML patients have genetic abnormalities that can be detected by more advanced techniques like NGS and CMA. These genetic abnormalities play a role in risk stratification that may remain hidden in otherwise CN-AML.
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Pinillos I, Pérez C, Torres O, Patarroyo MA, Bello FJ. Establishing and characterising a new cell line from Calliphora vicina (diptera: calliphoridae) fly embryonic tissues. Heliyon 2022; 8:e10674. [PMID: 36164515 PMCID: PMC9508484 DOI: 10.1016/j.heliyon.2022.e10674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/25/2022] [Accepted: 09/09/2022] [Indexed: 11/28/2022] Open
Abstract
Insect cell lines represent a promising and expanding field as they have several research applications including biotechnology, virology, immunity, toxicology, cell signalling mechanisms and evolution. They constitute a powerful tool having a direct impact on human and veterinary medicine and agriculture. Although more than 1000 cell lines have currently been established from various insect species, Calliphora vicina-derived fly cell lines are lacking. This study was aimed at establishing a new C. vicina embryonic tissue-derived cell line. Adult flies were collected and embryonated eggs were mechanically homogenised and seeded in four types of culture media (L15, Grace's insect medium, Grace's/L15 and DMEM). Cell growth and morphological characteristics were recorded and cytogenetic and molecular patterns were determined. The CV-062020-PPB cell line was established and was shown to have optimal growth in Grace's/L15 medium. CV-062020-PPB cell monolayers that had been sub-cultured over 16 times consisted of firmly adhering cells having different morphologies; a fibroblast-like shape dominated and the karyotype had a 12-chromosome diploid number. RAPD-PCR analysis of the CV-062020-PPB cell line revealed a high similarity index and strong intraspecific relationship with C. vicina adult flies and a weaker relationship with the Lutzomyia longipalpis-derived cell line (Lulo). The CV-062020-PPB cell line constitutes the first cell line obtained from C. vicina embryonic tissues and represents an important basic and applied research tool. A new C. vicina embryonic tissue-derived cell line is here reported. Fibroblast-like cells were predominant. The cell-line karyotype was 2n = 12 diploid chromosomes. The DNA profile enabled discriminating its molecular identity.
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