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Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community

Wise CA, Sullivan SG, Black ML, Erber WN, Bittles AH

Am. J. Phys. Anthropol., 2005 Nov;128(3):670-7.
PMID: 15864813

Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.

Matched MeSH terms: Chromosomes, Human, Y/genetics*
Fulltext Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, et al.

Curr Biol, 2019 01 07;29(1):149-157.e3.
PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029

The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.

Matched MeSH terms: Chromosomes, Human, Y/genetics*
Xga blood group in Chinese, Malays and Indians in Singapore

Saha N, Banerjee B

Vox Sang, 1973;24(6):542-4.
PMID: 4722836
Matched MeSH terms: Sex Chromosomes*
Fulltext X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma

Zuo XY, Feng QS, Sun J, Wei PP, Chin YM, Guo YM, et al.

Biol Sex Differ, 2019 03 25;10(1):13.
PMID: 30909962 DOI: 10.1186/s13293-019-0227-9

BACKGROUND: The male predominance in the incidence of nasopharyngeal carcinoma (NPC) suggests the contribution of the X chromosome to the susceptibility of NPC. However, no X-linked susceptibility loci have been examined by genome-wide association studies (GWASs) for NPC by far.
METHODS: To understand the contribution of the X chromosome in NPC susceptibility, we conducted an X chromosome-wide association analysis on 1615 NPC patients and 1025 healthy controls of Guangdong Chinese, followed by two validation analyses in Taiwan Chinese (n = 562) and Malaysian Chinese (n = 716).
RESULTS: Firstly, the proportion of variance of X-linked loci over phenotypic variance was estimated in the discovery samples, which revealed that the phenotypic variance explained by X chromosome polymorphisms was estimated to be 12.63% (non-dosage compensation model) in males, as compared with 0.0001% in females. This suggested that the contribution of X chromosome to the genetic variance of NPC should not be neglected. Secondly, association analysis revealed that rs5927056 in DMD gene achieved X chromosome-wide association significance in the discovery sample (OR = 0.81, 95% CI 0.73-0.89, P = 1.49 × 10-5). Combined analysis revealed rs5927056 for DMD gene with suggestive significance (P = 9.44 × 10-5). Moreover, the female-specific association of rs5933886 in ARHGAP6 gene (OR = 0.62, 95%CI: 0.47-0.81, P = 4.37 × 10-4) was successfully replicated in Taiwan Chinese (P = 1.64 × 10-2). rs5933886 also showed nominally significant gender × SNP interaction in both Guangdong (P = 6.25 × 10-4) and Taiwan datasets (P = 2.99 × 10-2).
CONCLUSION: Our finding reveals new susceptibility loci at the X chromosome conferring risk of NPC and supports the value of including the X chromosome in large-scale association studies.

Matched MeSH terms: Chromosomes, Human, X*
Whole-genome analysis of an extensively drug-resistant clinical isolate of Acinetobacter baumannii AC12: insights into the mechanisms of resistance of an ST195 clone from Malaysia

Lean SS, Yeo CC, Suhaili Z, Thong KL

Int J Antimicrob Agents, 2015 Feb;45(2):178-82.
PMID: 25481460 DOI: 10.1016/j.ijantimicag.2014.10.015

Acinetobacter baumannii has emerged as an important nosocomial pathogen owing to its increasing resistance to most, if not all, antibiotics in clinical use. We recently reported the occurrence of extensively drug-resistant (XDR) A. baumannii isolates in a Malaysian tertiary hospital. The genome of one of these XDR isolates (A. baumannii AC12) was completely sequenced and comparative genome analyses were performed to elucidate the genetic basis of its antimicrobial resistance. The A. baumannii AC12 genome consists of a 3.8 Mbp circular chromosome and an 8731 bp cryptic plasmid, pAC12. It belongs to the ST195 lineage and is most closely related to A. baumannii BJAB0715 as well as other strains of the international clone III (IC-III) group. Two antibiotic resistance islands (RIs), designated AC12-RI1 and AC12-RI2, were found in the AC12 chromosome along with a 7 kb Tn1548::armA island conferring resistance to aminoglycosides and macrolides. The 22.8 kb AC12-RI1 interrupts the comM gene and harbours the carbapenem resistance gene blaOXA-23 flanked by ISAba1 within a Tn2006-like structure. AC12-RI1 also harbours resistance determinants for aminoglycosides, tetracyclines and sulphonamides. The 10.3 kb IS26-flanked AC12-RI2 is a derivative of AbGRI2-1, containing aphA1b and blaTEM genes (conferring aminoglycoside and β-lactam resistance, respectively). The presence of numerous genes mediating resistance to various antibiotics in novel RI structures as well as other genes encoding drug transporters and efflux pumps in A. baumannii AC12 most likely contributed to its XDR characteristics.

Matched MeSH terms: Chromosomes, Bacterial
Fulltext Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2

Tharek M, Sim KS, Khairuddin D, Ghazali AH, Najimudin N

Genome Announc, 2017 May 11;5(19).
PMID: 28495774 DOI: 10.1128/genomeA.00305-17

Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We present here the whole-genome sequence of this plant-endophytic strain. The genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted coding sequences, and a G+C content of 50.8%.

Matched MeSH terms: Chromosomes
Fulltext Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae)

Adler PH, Takaoka H, Sofian-Azirun M, Low VL, Ya'cob Z, Chen CD, et al.

PLoS One, 2016;11(10):e0163881.
PMID: 27695048 DOI: 10.1371/journal.pone.0163881

The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country's status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam.

Matched MeSH terms: Polytene Chromosomes*
Variation in BCL2 protein expression in follicular lymphomas without t(14;18) chromosomal translocations

Masir N, Jones M, Abdul-Rahman F, Florence CS, Mason DY

Pathology, 2012 Apr;44(3):228-33.
PMID: 22406486 DOI: 10.1097/PAT.0b013e3283513fb2

The hallmark of follicular lymphoma is the t(14;18)(q32;q21) chromosomal translocations that lead to deregulation of BCL2 expression in tumour cells. However, not all cases of follicular lymphoma express BCL2, nor is the t(14;18) translocation always present. Follicular lymphomas lacking the BCL2 rearrangement are less well studied with regards to their immunohistochemical and molecular features. This study aims to investigate the BCL2 protein expression pattern in t(14;18) negative follicular lymphomas.

Matched MeSH terms: Chromosomes, Human, Pair 14*; Chromosomes, Human, Pair 18*
Fulltext Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution

Plissonneau C, Benevenuto J, Mohd-Assaad N, Fouché S, Hartmann FE, Croll D

Front Plant Sci, 2017;8:119.
PMID: 28217138 DOI: 10.3389/fpls.2017.00119

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.

Matched MeSH terms: Chromosomes
Fulltext Unbalanced chromosomal translocation: a cause of recurrent spontaneous abortion

Zarina AL, Jamil MA, Ng SP, Rohana J, Yong SC, Salwati S, et al.

Med J Malaysia, 2006 Jun;61(2):260-2.
PMID: 16898328 MyJurnal

Recurrent spontaneous abortion, defined as three consecutive abortions, occurs in approximately 1% to 2% of couples. Although the cause is unknown in up to 50% of cases, about 5% of these couples are found to be a balanced translocation carrier. We report a case in which the mother was identified to be a translocation carrier following the birth of a baby with multiple congenital abnormalities.

Matched MeSH terms: Chromosomes, Human, Pair 10*; Chromosomes, Human, Pair 15*
Fulltext Two cases of isochromosome 18q syndrome

Pal S, Siti MI, Ankathil R, Zilfalil BA

Singapore Med J, 2007 May;48(5):e146-50.
PMID: 17453088

Patients with isochromosome 18q, a rare cytogenetic abnormality, also reported as Edwards syndrome, is the second most common autosomal trisomy. However, the phenotypic features and survival of these patients are not uniform and depend upon the portion of chromosomes getting duplicated or deleted. The survival of these children may be longer, hence a good cytogenetic diagnosis is a must. Morphological characteristics of isochromosome 18q are not yet fully delineated because of the rarity of the cases and as most cases are aborted medically or terminate spontaneously. We report two cases of isochromosome 18q, one male aged two years old and the other a male aged eight months old, and review the literature on this rare syndrome.

Matched MeSH terms: Chromosomes, Human, Pair 18*
Fulltext Two cases of deletion 5p syndrome: one with paternal involvement and another with atypical presentation

Azman BZ, Akhir SM, Zilfalil BA, Ankathil R

Singapore Med J, 2008 Apr;49(4):e98-e100.
PMID: 18418516

We report two cases of deletion 5p or cri du chat syndrome (CdCS) with different presentations and risks of transmission: one case with paternal chromosome 5 involvement and another, a de novo case with atypical clinical presentation. Cytogenetic analysis was performed on the two cases and their parents. GTG-banded karyotype analysis of Cases 1 and 2 revealed abnormal 46,XY,del(5)(p13-15) male karyotypes. For Case 1, the mother showed normal female karyotype while the father showed an abnormal karyotype involving a balanced translocation 46,XY,t(5;10)(p13;p15). For Case 2, however, both parents showed a normal karyotype pattern. In Case 1, the clinical features, particularly the distinct facial phenotype in combination with a characteristic cat-like cry and hypotonia, aided in the diagnosis at birth and the karyotype analysis was resolutive. The boy in Case 2 presented with atypical clinical features. Even though this patient had multiple syndromic features, the typical high pitched cat-like cry was not prominent. Instead, the patient manifested persistent stridor (from day three of life), which might have prevented the clinician from suspecting CdCS at birth. However, when this patient was presented at seven months of age for cytogenetic analysis, a confirmatory diagnosis of CdCS was established. For children with congenital abnormalities, an early clinical diagnosis confirmed through cytogenetic and molecular investigations, is important for providing personalised diagnostic and prognostic evaluation, and also for genetic counselling on the reproductive risk, particularly for patients with parental chromosome translocation involvement.

Matched MeSH terms: Chromosomes, Human, Pair 5/genetics*
Fulltext Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome

Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, et al.

Genome Biol Evol, 2024 Mar 02;16(3).
PMID: 38408866 DOI: 10.1093/gbe/evae037

The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.

Matched MeSH terms: Sex Chromosomes/genetics
Fulltext Turner syndrome in diverse populations

Kruszka P, Addissie YA, Tekendo-Ngongang C, Jones KL, Savage SK, Gupta N, et al.

Am J Med Genet A, 2020 Feb;182(2):303-313.
PMID: 31854143 DOI: 10.1002/ajmg.a.61461

Turner syndrome (TS) is a common multiple congenital anomaly syndrome resulting from complete or partial absence of the second X chromosome. In this study, we explore the phenotype of TS in diverse populations using clinical examination and facial analysis technology. Clinical data from 78 individuals and images from 108 individuals with TS from 19 different countries were analyzed. Individuals were grouped into categories of African descent (African), Asian, Latin American, Caucasian (European descent), and Middle Eastern. The most common phenotype features across all population groups were short stature (86%), cubitus valgus (76%), and low posterior hairline 70%. Two facial analysis technology experiments were conducted: TS versus general population and TS versus Noonan syndrome. Across all ethnicities, facial analysis was accurate in diagnosing TS from frontal facial images as measured by the area under the curve (AUC). An AUC of 0.903 (p < .001) was found for TS versus general population controls and 0.925 (p < .001) for TS versus individuals with Noonan syndrome. In summary, we present consistent clinical findings from global populations with TS and additionally demonstrate that facial analysis technology can accurately distinguish TS from the general population and Noonan syndrome.

Matched MeSH terms: Chromosomes, Human, X/genetics
Fulltext Trisomy X and myelodysplastic syndrome (MDS) with eosinophilia

Eusni, R.M.T., Leong, C.F., Salwa, S.

Malaysian Journal of Medicine and Health Sciences, 2012;8(2):65-67.
MyJurnal

We reported a young patient with myelodysplastic syndrome (MDS) with eosinophilia, in which her chromosomal analysis revealed the presence of trisomy X and a marker chromosome at chromosome 11. The technique used to detect the chromosomal abnormalities is a multicoloured –fluorescent in situ hybridization technique (M-FISH). Our observation suggested that these underlying chromosomal abnormalities were probably responsible for her development of MDS with eosinophilia.
Myelodysplastic syndrome (MDS) is a condition whereby there is ineffective production of haematopoietic stem cells and poor quality of cells produced. The cause can either be a primary bone marrow problem, de novo or therapy related. Most MDS cases are secondary rather than primary. Many chromosomal abnormalities have been found in cases of myelodysplastic syndrome. We described a case of MDS with eosinophilia in association with presence of trisomy X and a marker chromosome in chromosome 11.

Matched MeSH terms: Chromosomes, Human, Pair 11; Chromosomes, Human, X
Fulltext Transcriptomic profiling of skeletal muscle from the Ts1Cje mouse model of Down syndrome suggests dysregulation of trisomic genes associated with neuromuscular junction signaling, oxidative stress and chronic inflammation

Leong, Melody Pui Yee, Usman Bala, Lim, Chai Ling, Rozita Rosli, Cheah, Pike-See, Ling, King-Hwa

Neuroscience Research Notes, 2018;1(1):21-41.
MyJurnal

Ts1Cje is a mouse model of Down syndrome (DS) with partial triplication of chromosome 16, which encompasses a high number of human chromosome 21 (HSA21) orthologous genes. The mouse model exhibits muscle weakness resembling hypotonia in DS individuals. The effect of extra gene dosages on muscle weakness or hypotonia in Ts1Cje and DS individuals remains unknown. To identify molecular dysregulation of the skeletal muscle, we compared the transcriptomic signatures of soleus and extensor digitorum longus (EDL) muscles between the adult Ts1Cje and disomic littermates. A total of 166 and 262 differentially expressed protein-coding genes (DEGs) were identified in the soleus and EDL muscles, respectively. The partial trisomy of MMU16 in Ts1Cje mice has a greater effect on gene expression in EDL. Top-down clustering analysis of all DEGs for represented functional ontologies revealed 5 functional clusters in soleus associated with signal transduction, development of reproductive system, nucleic acid biosynthesis, protein modification and metabolism as well as regulation of gene expression. On the other hand, only 3 functional clusters were observed for EDL namely neuron and cell development, protein modification and metabolic processes as well as ion transport. A total of 11 selected DEGs were validated using qPCR (disomic DEGs: Mansc1; trisomic DEGs: Itsn1, Rcan1, Synj1, Donson, Dyrk1a, Ifnar1, Ifnar2, Runx1, Sod1 and Tmem50b). The validated DEGs were implicated in neuromuscular junction signalling (Itsn1, Syn1), oxidative stress (Sod1, Runx1) and chronic inflammation processes (Runx1, Rcan1, Ifnar1, Ifnar2). Other validated DEGs have not been well-documented as involved in the skeletal muscle development or function, thus serve as interesting novel candidates for future investigations. To our knowledge, the study was the first attempt to determine the transcriptomic profiles of both soleus and EDL muscles in Ts1Cje mice. It provides new insights on the possible disrupted molecular pathways associated with hypotonia in DS individuals.

Matched MeSH terms: Chromosomes, Human, Pair 16
Fulltext Towards complete and error-free genome assemblies of all vertebrate species

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.

Nature, 2021 Apr;592(7856):737-746.
PMID: 33911273 DOI: 10.1038/s41586-021-03451-0

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Matched MeSH terms: Sex Chromosomes/genetics
Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Khan FA, Phillips CD, Baker RJ

Syst Biol, 2014 Jan 1;63(1):96-110.
PMID: 24149076 DOI: 10.1093/sysbio/syt062

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLPs) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about 3 Ma, with ongoing hybridization between mitochondrial lineages separated by 2.5 myr. The timeframe of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

Matched MeSH terms: Sex Chromosomes/genetics
Fulltext Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21

Zhang M, Wang Z, Obazee O, Jia J, Childs EJ, Hoskins J, et al.

Oncotarget, 2016 Oct 11;7(41):66328-66343.
PMID: 27579533 DOI: 10.18632/oncotarget.11041

Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology.

Matched MeSH terms: Chromosomes, Human, Pair 1/genetics*; Chromosomes, Human, Pair 5/genetics*; Chromosomes, Human, Pair 8/genetics*
Fulltext The various effect s of Nigella sativa on multiple body systems in human and animals

Mohammed Abdulrazzaq Assi

The Pertanika Journal of Scholarly Research Reviews, 2016;2(3):0-0.
MyJurnal

Nigella sativa (Black seeds) has been recognized as one of the most popular herbs in many
parts of the world for centuries. It was used in the world as folk medicine to cure different kinds of diseases. This plant has been considered as one of the main sources of nutrition and healthcare for humans as well as animals. It has been perceived as Kalonji; it is a southwest Asian plan t that flowers annually. The seeds and oil of this plant have been used in food; in addition, it has a long history in the making of medicines. In addition to its being a model plant for better realization of gene and chromosome relationship, the plant species is also significant cytogenetically. Plant based system has not been absorbed fully for human health care despite the remarkable advancements in the field of pharmacology. Cumin, as one of the medicinal plants gifted to humans by nature, has a number of potential uses. It has been proved to be a
useful herbal medicines that can be used for human health and therefore has been extensively studied and investigated to further discover the advantages of this plant.

Matched MeSH terms: Chromosomes

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