A unique Y gene in the Asian malaria mosquito Anopheles stephensi encodes a small lysine-rich protein and is transcribed at the onset of embryonic development

In many organisms the Y chromosome initiates sex determination and regulates male fertility and mating behaviour. However, molecular characterization of Y genes is rare outside of a few model species because it is difficult to clone and analyse repeat-rich heterochromatic Y sequences. In insects, Y genes are only well characterized in a small number of Drosophila species. Here we report the discovery of GUY1 (gene unique to the Y), a gene unique to the Y chromosome in the Asian malaria mosquito, Anopheles stephensi, using an approach that compares Illumina sequences separately obtained from male and female genomic DNA. Experimental evidence confirmed that GUY1 is a single copy gene found only on the Y chromosome. GUY1 is transcribed at the very onset of zygotic transcription and encodes a small lysine-rich protein that forms two alpha helices and shows DNA-binding properties. Interestingly, three helix-loop-helix proteins are key factors that determine sex in the early embryo in Drosophila melanogaster. Single embryo analysis indicated that GUY1 is only transcribed in male embryos and that the GUY1 promoter is functional in the early embryos. GUY1 may be used as a paternally inherited molecular marker. Further investigation of GUY1 will contribute to the genetic approaches to control mosquito-borne diseases.

Success rate of microsurgical multiple testicular sperm extraction and sperm presence in the ejaculate in korean men with y chromosome microdeletions

PURPOSE

We assessed the frequency of azoospermia factor a (AZFa), AZFb, and AZFc deletions and examined correlations between the deletion sites and the success rates of sperm presence within the ejaculate and surgical sperm retrieval in Korean men.

MATERIALS AND METHODS

A total of 1,919 azoospermic and severely oligozoospermic men were assessed for Y chromosome microdeletions. Among them, 168 men with AZF deletions were identified and their medical records were reviewed.

RESULTS

Of the total 168 men with AZF deletions, there were 13 with AZFa, 10 with AZFb, 95 with AZFc, 37 with AZFbc, and 13 with AZFabc deletions. Of the 95 men with isolated AZFc deletion, 51 had the presence of sperm in the ejaculate. Of the infertile men with any other deletion, however, only two patients (one man with AZFb deletion and another with AZFbc deletion) showed the presence of sperm in the ejaculate. The success rates for surgical sperm retrieval were 7.1% (1/14) in men with AZFbc deletion and 54.8% (17/31) in the isolated AZFc deletion group. No sperm was obtained from the patients with AZFa or AZFb deletions who underwent microsurgical sperm retrieval. In the isolated AZFc deletion group, there were significant differences between azoospermic and severely oligozoospermic patients in terms of testicular volume and serum levels of follicle-stimulating hormone and luteinizing hormone, whereas no significant differences were found when the group was divided by surgical sperm retrieval outcomes.

CONCLUSIONS

Deletions of the AZFa and AZFb regions are associated with severe spermatogenetic impairment. However, more than half of men with an AZFc deletion had sperm within the ejaculate or testis for in vitro fertilization with intracytoplasmic sperm injection.

Surname distribution in population genetics and in statistical physics

Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents.

Chromatin-associated proteins HP1 and Mod(mdg4) modify Y-linked regulatory variation in the drosophila testis

Chromatin remodeling is crucial for gene regulation. Remodeling is often mediated through chemical modifications of the DNA template, DNA-associated proteins, and RNA-mediated processes. Y-linked regulatory variation (YRV) refers to the quantitative effects that polymorphic tracts of Y-linked chromatin exert on gene expression of X-linked and autosomal genes. Here we show that naturally occurring polymorphisms in the Drosophila melanogaster Y chromosome contribute disproportionally to gene expression variation in the testis. The variation is dependent on wild-type expression levels of mod(mdg4) as well as Su(var)205; the latter gene codes for heterochromatin protein 1 (HP1) in Drosophila. Testis-specific YRV is abolished in genotypes with heterozygous loss-of-function mutations for mod(mdg4) and Su(var)205 but not in similar experiments with JIL-1. Furthermore, the Y chromosome differentially regulates several ubiquitously expressed genes. The results highlight the requirement for wild-type dosage of Su(var)205 and mod(mdg4) in enabling naturally occurring Y-linked regulatory variation in the testis. The phenotypes that emerge in the context of wild-type levels of the HP1 and Mod(mdg4) proteins might be part of an adaptive response to the environment.

Are there fetal stem cells in the maternal brain?

Fetal cells can enter maternal blood during pregnancy but whether they can also cross the blood-brain barrier to enter the maternal brain remains poorly understood. Previous results suggest that fetal cells are summoned to repair damage to the mother's brain. If this is confirmed, it would open up new and safer avenues of treatment for brain damage caused by strokes and neural diseases. In this study, we aimed to investigate whether a baby's stem cells can enter the maternal brain during pregnancy. Deceased patients who had at least one male offspring and no history of abortion and blood transfusion were included in this study. DNA was extracted from brain tissue samples of deceased women using standard phenol-chloroform extraction and ethanol precipitation methods. Genomic DNA was screened by quantitative fluorescent-polymerase chain reaction amplification together with short tandem repeat markers specific to the Y chromosome, and 13, 18, 21 and X. Any foreign DNA residues that could be used to interpret the presence of fetal stem cells in the maternal brain were monitored. Results indicated that fetal stem cells can not cross the blood-brain barrier to enter the maternal brain.

Detection of Y Chromosome Microdeletion is Valuable in the Treatment of Patients With Nonobstructive Azoospermia and Oligoasthenoteratozoospermia: Sperm Retrieval Rate and Birth Rate

Purpose

We evaluated clinical characteristics, sperm retrieval rates, and birth rates in a relatively large number of infertile patients with Y chromosome microdeletions.

Materials and Methods

We retrospectively reviewed clinical data from 213 patients with nonobstructive azoospermia (NOA) and 76 patients with oligoasthenoteratozoospermia (OATS) who were tested for Y chromosome microdeletion from March 2004 to June 2011.

Results

Of the 289 patients, 110 patients presented with Y chromosome microdeletion and 179 patients presented with no microdeletion. Among the patients with Y chromosome microdeletions, 83/110 (75.4%) were NOA patients and 27/110 (24.5%) were OATS patients. After subdividing the patients with Y chromosome microdeletion, 29 had azoospermia factor (AZF)b-c microdeletion and 81 had AZFc microdeletion. The sperm retrieval rate was similar between patients with Y chromosome microdeletion and those with no microdeletion (26.6% vs. 25.6%, p=0.298) after multiple testicular sperm extraction (TESE). Excluding 53 patients who did not undergo TESE, 30 patients were analyzed. All of the 9 men with AZFb-c microdeletion had a complete absence of sperm despite multiple TESE. However, multiple TESE was successful for 9 of 21 patients with only AZFc microdeletion (p=0.041). Twenty patients with Y chromosome microdeletion gave birth.

Conclusions

In NOA and OATS patients, no significant difference in the sperm retrieval rate was shown between patients with Y chromosome microdeletion and those with no microdeletion. Patients with short Y chromosome microdeletion such as AZFc microdeletion have better prognoses for sperm retrieval and an increased chance of conception than do patients with larger microdeletions such as AZFb-c microdeletion.

The utility of mitochondrial and y chromosome phylogenetic data to improve correction for population stratification

Genome-wide association (GWA) studies have become a standard approach for discovering and validating genomic polymorphisms putatively associated with phenotypes of interest. Accounting for population structure in GWA studies is critical to attain unbiased parameter measurements and control Type I error. One common approach to accounting for population structure is to include several principal components derived from the entire autosomal dataset, which reflects population structure signal. However, knowing which components to include is subjective and generally not conclusive. We examined how phylogenetic signal from mitochondrial DNA (mtDNA) and chromosome Y (chr:Y) markers is concordant with principal component data based on autosomal markers to determine whether mtDNA and chr:Y phylogenetic data can help guide principal component selection. Using HAPMAP and other original data from individuals of multiple ancestries, we examined the relationships of mtDNA and chr:Y phylogenetic signal with the autosomal PCA using best subset logistic regression. We show that while the two approaches agree at times, this is independent of the component order and not completely represented in the Eigen values. Additionally, we use simulations to demonstrate that our approach leads to a slightly reduced Type I error rate compared to the standard approach. This approach provides preliminary evidence to support the theoretical concept that mtDNA and chr:Y data can be informative in locating the PCs that are most associated with evolutionary history of populations that are being studied, although the utility of such information will depend on the specific situation.

An assay to detect in vivo Y chromosome loss in Drosophila wing disc cells

Loss of the Y chromosome in Drosophila has no impact on cell viability and therefore allows us to assay the impact of environmental agents and genetic alterations on chromosomal loss. To detect in vivo chromosome loss in cells of the developing Drosophila wing primordia, we first engineered a Y chromosome with an attP docking site. By making use of the ΦC31 integrase system, we site-specifically integrated a genomic transgene encompassing the multiple wing hair (mwh) locus into this attP site, leading to a mwh⁺Y chromosome. This chromosome fully rescues the mwh mutant phenotype, an excellent recessive wing cell marker mutation. Loss of this mwh⁺Y chromosome in wing primordial cells then leads to manifestation of the mwh mutant phenotype in mwh-homozygous cells. The forming mwh clones permit us to quantify the effect of agents and genetic alterations by assaying frequency and size of the mwh mosaic spots. To illustrate the use of the mwh⁺Y loss system, the effects of four known mutagens (X-rays, colchicine, ethyl methanesulfonate, and formaldehyde) and two genetic conditions (loss- and gain-of-function lodestar mutant alleles) are documented. The procedure is simple, sensitive, and inexpensive.

SRY sequence in maternal plasma: Implications for non-invasive prenatal diagnosis: First report from India

AIM:

The presence of circulatory cell-free fetal DNA in maternal plasma has found new applications in non-invasive risk-free prenatal diagnosis.

MATERIALS AND METHODS:

We made use of a size separation approach along with real time polymerase chain reaction (PCR) to evaluate the use of fetal DNA in the detection of the sex of the fetus. Cell-free fetal DNA was isolated from the plasma of 30 women (10–20 weeks gestation) using a size separation approach. We made use of Taq Man Chemistry and real time PCR using primers and probes for GAPDH and SRY.

RESULTS:

Only 24 cases could be studied as there was no amplification in six cases. Fetal sex was accurately determined in all of the 24 cases wherein 19 women were carrying male fetuses and five women were carrying female fetuses. An increase in the amount of fetal DNA was observed with an increase in the gestational age.

CONCLUSIONS:

Real time PCR analysis is a highly sensitive and accurate tool for non-invasive prenatal diagnosis, allowing detection of the sex of the fetus as early as 10 weeks of gestation. Non-invasive prenatal diagnosis eliminates the risk of fetal loss associated with the invasive procedure.

Additional Y-STRs in Forensics: Why, Which, and When

Male-specific DNA profiling using nonrecombining Y-chromosomal genetic markers is becoming ubiquitous in forensic genetics, with many laboratories and jurisdictions taking advantage of the benefits that Y-chromosome short tandem repeat (Y-STR) profiling can bring. The current suite of 9-17 core Y-STRs, available as commercial kits, perform adequately for identifying male lineages in many populations, a feature highly suitable for excluding a male suspect from involvement in crimes such as sexual assaults where autosomal STR profiling is often troubled. However, there is a growing need to achieve higher resolution in paternal-lineage differentiation as adventitious matches between unrelated males are becoming increasingly common with the increasing size of Y-STR haplotype-frequency databases. Furthermore, with the currently used Y-STRs, male relatives (both close and distant) usually cannot be separated, marking a strong limitation in forensic applications as conclusions cannot be drawn on the individual level as desired. Performing Y-chromosome analysis in familial testing, which outperforms autosomal STR profiling in certain deficiency cases, with the current Y-STR sets can be troubled by mutations that complicate relationship-probability estimations. To overcome these limitations, considerable research has been performed over recent years to identify and characterize additional Y-STRs. This review summarizes the forensic performance of current sets of Y-STRs, points out their limitations in the three main areas of forensic Y-STR applications (male-lineage differentiation, male-relative differentiation, and paternity/familial testing), and discusses why and which additional Y-STRs are suitable to improve forensic Y-chromosome analysis in the future.

Y chromosome microdeletions in sperm DNA of infertile patients from Tamil Nadu, south India

Context:

Y chromosome microdeletions in infertile men of Tamil Nadu, South India.

Aim:

The paper assesses the association of Y chromosome microdeletions among infertile patients using several STS markers from each AZF (AZoospermic Factor) region and also aspires to determine whether the blood DNA microdeletion picture matches the semen DNA Yq microdeletion map.

Materials and Methods:

A total of 287 men, including 147 infertile men and 140 normozoospermic fertile controls were included for the study.

Results:

Screening 72 semen samples with the STS markers specific to AZF (a,b,c) regions showed Y chromosome microdeletions in 19 (12.9%) individuals. No deletion was observed in all the three AZF regions by screening 45 blood and 30 paired samples. None of the control men showed deletion for the 28 STS markers, which were used for the primary screening of the deletion of AZF a,b,c regions.

Conclusion:

Germ cell DNA can be analyzed for Yq microdeletions rather than blood DNA.

Genetic and epigenetic factors: Role in male infertility

Genetic factors contribute upto 15%-30% cases of male infertility. Formation of spermatozoa occurs in a sequential manner with mitotic, meiotic, and postmeiotic differentiation phases each of which is controlled by an intricate genetic program. Genes control a variety of physiologic processes, such as hypothalamus-pituitary-gonadal axis, germ cell development, and differentiation. In the era of assisted reproduction technology, it is important to understand the genetic basis of infertility to provide maximum adapted therapeutics and counseling to the couple.

Azoospermia factor and male infertility

Recently, work has shown that azoospermia factor (AZF) microdeletions result from homologous recombination between almost identical blocks in this gene region. These microdeletions in the Y chromosome are a common molecular genetic cause of spermatogenetic failure leading to male infertility. After completion of the sequencing of the Y chromosome, the classical definition of AZFa, AZFb, and AZFc was modified to five regions, namely AZFa, P5/proximal-P1, P5/distal-P1, P4/distal-P1, and AZFc, as a result of the determination of Y chromosomal structure. Moreover, partial AZFc deletions have also been reported, resulting from recombination in their sub-ampliconic identical pair sequences. These deletions are also implicated in a possible association with Y chromosome haplogroups. In this review, we address Y chromosomal complexity and the modified categories of the AZF deletions. Recognition of the association of Y deletions with male infertility has implications for the diagnosis, treatment, and genetic counseling of infertile men, in particular candidates for intracytoplasmic sperm injection.

Effect of granulocyte colony stimulating factor on repair of CCl4-induced liver injury in mice

AIM: To observe the effect of recombinant human granulocyte colony stimulating factor (rhG-CSF) on repair of CCl4-induced liver injury in mice, and to investigate the homing ability of peripheral blood stem cells mobilized by rhG-CSF to localize in the injured liver.

METHODS: Liver injury was induced by 400 mL/L CCl₄ 2 mL/kg in clean BALB/c mice twice a week and then treated. Then, with rhG-CSF 200 µg/kg sc. The mortality rate and liver pathology changes and liver functions and other factors were analyzed. Detection of CD34⁺ and Thy-1⁺ cells were performed with flow-cytometry and immunohistochemical staining respectively. The situ hybridization for Y chromosome in liver was tested to determine the homing ability of the peripheral blood stem cells of male mice mobilized by rhG-CSF to the injured liver of female mice.

RESULTS: Compared with the liver injury group, the mortality rate and changes in liver histology and function in the rhG-CSF prevention group were significantly lower (P < 0.05). Alanine aminotransferase and aspartate aminotransferase were significantly lower in the rhG-CSF treatment group at 30 days after CCl4 discontinuation than in the control group (1033.5 ± 350.1 nkat/L vs 1983.7 ± 616.8 nkat/L, P < 0.01; 1817.0 ± 483.4 nkat/L 3017.3 ± 811.2 nkat/L, P < 0.05). Compared with the control group, Thy-1⁺ and CD34⁺ cells in the liver of the rhG-CSF treatment group were increased on days 8 and 15 (P < 0.05). In situ hybridization in the liver of female mice transplanted with peripheral stem cells from male mice revealed that Y-chromosome- positive cells were found in the injured liver, which were mainly seen around the duct area and central vein, and a few in the spleen.

CONCLUSION: rhG-CSF prevention and treatment significantly promote recovery and improve survival after CCl₄-induced liver injury.

Y chromosome and new concept of azoospermia factor

The completion of a draft sequence of the entire human genome in 2001 was followed by a complete sequencing of the Y chromosome in 2003. It is now possible to refer to a physical map of the Y chromosome. The Y chromosome can be classified into X-transposed, X-degenerate and ampliconic sequences depending on the origins of its sequences. In particular, the ampliconic sequences are complexes of massive palindrome structures in which sequences having higher than 99.9% homology are present symmetrically. Interestingly, palindromic repeats may undergo frequent gene conversion associated with intrachromosomal recombination and play an important role in the maintenance of the genetic materials of the Y chromosome. The azoospermia factor (AZF) region of the ampliconic region is the most probable candidate for spermatogenesis, and forms a palindrome structure. Thus, there is a limit in the detection of microdeletion using conventional sequence-tagged sites based on polymerase chain reaction because of their structure. It is now necessary to update the AZF concept. (Reprod Med Biol 2005; 4: 123-128).

Genetic Markers in Human Bone Tissue

The use of genetic markers in bone and tissues as a method of human identification is reviewed in detail. Methods for the identification of human remains and the case situations requiring them are described. Some of the previous work on tissue and bone ABO grouping from both anthropological and medicolegal perspectives is reviewed; and some results from our own studies that have produced a highly reliable bone grouping procedure are presented. Some of our work and that of others on the typing of other classical genetic marker systems in bone is included. Recent work on DNA polymorphism typing and some actual and potential forensic applications of bone (and tissue) deoxyribonucleic acid (DNA) typing are discussed.