Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant

An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.

Functional characterization of a natural variant of luteinizing hormone

Luteinizing hormone (LH) plays an important role in the gametogenesis in both sexes by promoting the production of sex steroid hormones in the testes and ovaries. We previously described a genetic variant (V) of LH resulted from a mutation (G1502A) in the LH beta-subunit gene, causing the glycine102serine change in the protein hormone. This variant was subsequently found to be associated with both male and female infertility. In this study, we determined the functional aspect of this LH variant in vitro. Site-directed mutagenesis was employed to construct the V-LH beta-subunit gene. Bioactivities of V-LH expressed in Chinese hamster ovary (CHO) cells cotransfected with the V-beta-subunit and native alpha-subunit genes were compared to those of wild-type (WT) LH. The amino acid replacement did not result in the change of efficacy of alpha- and beta-subunit dimerization of the hormone. However, V-LH had significantly lower receptor-binding activity (P<0.001) and lower biopotency for progesterone production (P<0.001) than WT-LH at the higher concentrations of LH. Considering the latter and its known association with both male and female infertility, it is suggested that the V-LH may be a contributing factor to the pathogenesis of infertility in the carriers of this variant.

Absence of mutations in the coding regions of follicle-stimulating hormone receptor gene in Singapore Chinese women with premature ovarian failure and polycystic ovary syndrome

Normal gonadal function is critically dependent on the integrity of pituitary-gonadal axis, where follicle-stimulating hormone (FSH) plays a key role. In the female, FSH is required for follicular growth, estrogen production and oocyte maturation. Its function is mediated by its specific receptor (FSHR), and defective FSHR has been shown to affect folliculogenesis and ovarian function. In this study, we screened the entire coding region of FSHR gene for pathogenic mutations in women with premature ovarian failure (POF) (n = 16) and polycystic ovary syndrome (PCOS) (n = 124) and found no mutations in these patients. Two known polymorphisms, Thr307Ala and Ser680Asn showed similar distributions of the allelic variations and protein isoforms in PCOS and normal control subjects (n = 236). It appears from this study that mutations in the coding regions of FSHR gene are not a causative factor of the above clinical manifestations in Chinese Singapore women.

Association between estrogen receptor-beta gene polymorphisms and ovulatory dysfunctions in patients with menstrual disorders

Estrogen plays a significant role in human ovulation. It acts as an important positive regulator of the preovulatory gonadotropin surge necessary to initiate the cascade of events leading to ovulation. The steroid hormone exerts its physiological responses through the estrogen receptor (ER), of which two subtypes, ERalpha and ERbeta, are known. ERbeta messenger ribonucleic acid occurs maximally in the ovaries and granulosa cells; thus, ERbeta may be essential for normal ovulation. In a recent gene knockout study, it has been shown that ERbeta gene null female mice develop normal reproductive tract and ovaries during pre- and neonatal periods, but have an abnormal frequency of spontaneous ovulation in adulthood. In the present case-control study, we explored the association of two recently described ERbeta gene polymorphisms, RSAI and ALUI, with ovulatory dysfunctions. The respective frequencies of these polymorphisms were significantly higher in patients than in controls (P= 0.009 and P= 0.059). The polymorphisms were significantly associated with ovulatory dysfunctions, especially in patients homozygous for the polymorphisms (P = 0.016 and P = 0.038, respectively). The compound homozygosity of the polymorphisms was seen only in patients (n = 5) and not controls (P = 0.009). The serum levels of LH, FSH, and progesterone were lower in the homozygous and compound homozygous than in the respective nonpolymorphic patients. All five compound homozygous patients had ovulatory dysfunctions with no etiological pathology. Our results suggest that ERbeta gene RSA:I and ALU:I polymorphisms may be associated with ovulatory defects in some patients, especially those with unknown causes.

Association of AccI polymorphism in the follicle-stimulating hormone beta gene with polycystic ovary syndrome

OBJECTIVE

To search for FSH beta-subunit gene mutations in patients with polycystic ovary syndrome (PCOS) and determine the association between the mutations and the syndrome.

DESIGN

Clinical and molecular studies.

SETTING

Clinics and laboratories of the National University Hospital Obstetrics and Gynecology Department in Singapore.

PATIENT(S)

One hundred thirty-five patients with PCOS and 105 normal control subjects.

INTERVENTION(S)

Exons two and three were screened for mutations by single-stranded conformational polymorphism and DNA sequencing.

MAIN OUTCOME MEASURE(S)

Polymerase chain reaction followed by restriction enzyme analysis.

RESULT(S)

No missense mutation was found in the functional units of the FSHbeta gene in patients with PCOS, but a thymine-cytosine substitution in exon 3 (codon 76, TAT to TAC) was identified. The nucleotide change led to creation of an AccI digestion site. The distribution pattern of AccI polymorphism in the patients was significantly different from that in the control group, and the occurrence of homozygous carriers was significantly higher in patients (12.6%) than in the control group (3.8%). The frequency of polymorphism and prevalence of homozygosity were significantly higher in patients with PCOS with obesity (0.50% and 31.0%, respectively) than in those with menstrual disorders only (0.366% and 8.5%, respectively), which correlated with significantly higher androgen levels in the obese patients.

CONCLUSION(S)

The AccI polymorphism in FSHbeta gene may be associated with PCOS in some women, especially those with obesity.

Preliminary investigation of follistatin gene mutations in women with polycystic ovary syndrome

Strong evidence for a link between the follistatin gene and polycystic ovary syndrome (PCOS) has recently been found in a well-designed large-scale study. Follistatin binds to activin and affects its functions, e.g. stimulation of FSH synthesis and secretion. Thus, it may play a role in the functional impairment of the FSH-granulosa cell axis in PCOS. In this study, we screened 64 Chinese patients with PCOS for mutations in the entire coding region (including the region encoding alternative carboxy-terminals) of the follistatin gene using polymerase chain reaction (PCR)-based single-stranded conformational polymorphism (SSCP) and DNA sequencing. However, we could not identify a single mutation of either the activating or inhibiting type, using these techniques. Therefore, it would appear that PCOS in the local Chinese population is not caused by mutations in the coding regions of the follistatin gene.

Association of molecular variants of luteinizing hormone with male infertility

Luteinizing hormone (LH) stimulates the interstitial Leydig cells to produce testosterone, which is essential for spermatogenesis. Abnormalities in the function of LH may affect the process of spermatogenesis and thus result in infertility. The aim of this study was to determine the association of three known variants of LH (Gln54Arg [Trp8Arg; Ile15Thr] and Gly102Ser) with male infertility. A total of 145 infertile men and 200 healthy fertile men were recruited and screened for the presence of these three LH variants. The Gln54Arg variant could not be detected in either of the groups studied. Twelve infertile (8.2%) and 15 fertile (7.5%) men were found to carry the [Trp8Ile; I15Thr] variant, but its occurrence did not show any significant difference between the patient and control groups. The Gly102Ser variant was detected in five patients with infertility (3.4%), but not in the control subjects (P = 0.013). This study showed that the Gln54Arg and [Trp8Ile; I15Thr] variants in the LHbeta gene were not associated with male infertility, whereas the Gly102Ser variant might be implicated in infertility in some Singapore Chinese men.

Mitochondrial gene mutations in gestational diabetes mellitus

Mitochondrial DNA mutations have been implicated in many diseases including diabetes mellitus. Although gestational diabetes mellitus (GDM) has been suggested to have genetic determinant and to be etiologically indistinct with non-insulin-dependent diabetes mellitus (NIDDM), its association with mitochondrial gene mutations is still unknown. In this study, 137 patients with GDM and 292 non-diabetic pregnant controls were examined for mitochondrial DNA mutations from the nucleotide 3130-4260 encompassing tRNA-Leu gene and adjacent NADH dehydrogenase 1 gene by polymerase chain reaction, single-stranded conformation polymorphism, restriction fragment length polymorphism and DNA sequencing. One heteroplasmic mutation at the position of 3398 (T-C), which changed a highly conserved methionine to threonine in NADH dehydrogenase subunit 1, was identified in 2.9% GDM patients but not in the controls, indicating its association with GDM (P = 0.01). Two novel mutations, a heteroplasmic C3254A and a homoplasmic A3399T, were also found in GDM subjects, the functional meaning of which merits further investigation. G3316A and T3394C mutations implicated in NIDDM, were seen at higher frequencies in patients with GDM than the controls. Our results suggest that mitochondrial DNA mutations may contribute to the development of GDM in some patients.

Association of molecular variants of luteinizing hormone with menstrual disorders

OBJECTIVE

Luteinizing hormone (LH) promotes ovulation and luteinization of the ovarian follicle, and stimulates steroidogenesis in the ovaries. It is known to be present in different molecular forms, and secretion of abnormal LH has been implicated in menstrual disorders and infertility. The purpose of this study was to determine any association of two recently described LH variants with menstrual disorders in Singapore Chinese women. One of these variants had Trp8 to Arg8 and Ile15 to Thr15 replacements in the LH beta-subunit, while the second variant possessed Ser102 substitution for Gly102.

PATIENTS

One hundred and seventy six patients with menstrual disorders and two hundred normal ovulatory women were recruited and screened for the presence of these two LH variants.

METHODS

The polymerase chain reaction (PCR) products of patients were analysed by restriction fragment length polymorphism (RFLP) and the results were compared with those of normal ovulatory women and confirmed by DNA sequencing.

RESULTS

Twenty one (11.9%) patients with menstrual disorders and twenty (10%) normal ovulatory women were found to carry the first variant, but its occurrence did not show any significant statistical difference between the patient and control groups (P = 0.679). However, the second variant was only detected in seven (4%) patients with menstrual disorders, and none of the normal ovulatory subjects (P = 0.005).

CONCLUSIONS

the study showed that the first variant was not associated with menstrual disorders, whereas the second variant might be implicated in menstrual disorders in some Singapore Chinese women.

New AccI polymorphism in the follicle-stimulating hormone beta-subunit gene and its prevalence in three Southeast Asian populations

A thymine-cytosine substitution was identified in exon 3 (codon 76, TAT to TAC) of the human follicle-stimulating hormone (FSH) beta-subunit gene. The nucleotide change led to creation of an AccI digestion site. The frequencies of the A allele (with AccI site) in Chinese (n = 201), Malays (n = 168) and Indians (n = 132) were 0.358, 0.333 and 0.402, respectively. The new FSH beta-subunit marker may be useful in gene tracking and association studies.

Molecular variants of luteinizing hormone in three populations of Southeast Asia

Three populations of Southeast Asia comprising 191 Chinese, 121 Malays and 150 Indians, were studied with respect to two recently described mutant luteinizing hormone (LH) variants using molecular techniques. One of these variants had Trp8 to Arg8 and Ile15 to Thr15 replacements in exon 2 of the LH beta-subunit, while the other variant possessed Ser102 substitution for Gly102 in exon 3. The exon 2 mutants were in complete linkage disequilibrium. The exon 2 variant had an allele frequency of 0.045 in Chinese, 0.062 in Malays and 0.030 in Indians. The allele frequency of the exon 3 variant was 0.018 in Chinese and null in Malays and Indians. The two LH variants may be markers of interest in studies of disturbed pituitary-gonadal function, menstrual disorders and female infertility.

A new molecular variant of luteinizing hormone associated with female infertility

OBJECTIVE

To investigate whether the newly described G1502 to A1502 mutation in exon 3 of the LH beta-subunit gene, causing the amino acid substitution of Ser102 for Gly102, is related to female infertility.

DESIGN

Screening of fertile and infertile women for the G1502 to A1502 mutation in the LH beta-subunit gene.

SETTING

Clinics and laboratories of the National University Hospital obstetrics and gynecology department, Singapore.

PATIENT(S)

Two hundred twelve healthy fertile women; 40 infertile women with menstrual disorders, polycystic ovary syndrome, and endometriosis; and 12 women with idiopathic infertility.

INTERVENTION(S)

Exon 3 of the LH beta-subunit gene was analyzed using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and PCR-mediated direct DNA sequencing.

MAIN OUTCOME MEASURE(S)

The PCR products of patients were analyzed by RFLP, and the results were compared with those of fertile controls. DNA sequencing radiographs were compared between two mutation-bearing patients and four controls.

RESULT(S)

The mutation was identified in only two infertile women with endometriosis; other women studied were found to be negative for this mutation.

CONCLUSION(S)

The missense mutation in the LH beta-subunit gene may be implicated in female infertility, possibly endometriosis-associated infertility in some women.

Identification of seven novel mutations in LH beta-subunit gene by SSCP

Seven new point mutations have been identified from LH beta-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.

Organization of the XYL genes in a thermophilic Bacillus species

The organization of the genes involved in xylose catabolism in a thermophilic Bacillus sp. LW2 was found to be different from that of mesophiles such as B. subtilis and Escherichia coli. We have reported previously the cloning and characterization of the xylose isomerase gene (xylA) from this thermophilic Bacillus sp. A xylose transport permease gene (xylP) was located immediately upstream of xylA. This gene encoded a hydrophobic protein (392 amino acids) with a calculated molecular weight of 42,307. Further upstream of xylP, another related gene xylO encoding a sugar transport ATP-binding protein was observed. A xylulose kinase gene (xylB) was identified downstream of xylA. Its open reading frame extended up to 1122 bp and represented a part (372 aa) of the enzyme. The order of the xyl genes in the thermophilic Bacillus sp. is therefore 5'-xylO (ATP-binding protein)-xylP (xylose permease)-xylA (xylose isomerase)-xylB (xylulose kinase)-3'. The polarity of expression of these four genes was found to be unidirectional from xylO to xylB.

Molecular cloning and characterization of the xylose isomerase gene from a thermophilic Bacillus species

The gene (xylA) encoding a thermostable xylose isomerase has been isolated and characterized from a thermophilic Bacillus species for the first time. The xylA open reading frame of 1323 bp encoded a protein containing 441 amino acids with a calculated molecular weight of 50,176. The amino acid sequence of this protein showed 76% homology to xylose isomerase isolated from Bacillus subtilis and contained all the important catalytic domains of the enzyme. The gene complemented the xyl-5 mutation and produced a functional enzyme constitutively in Escherichia coli. The crude cell-free extract of E. coli recombinants exhibited xylose isomerase activity over a wide range of temperatures from 60 to 100 degrees C with an optimal enzyme activity of 10.4 Units/mg protein at 85 degrees C. This optimal temperature was one of the highest reported so far for thermostable xylose isomerases. The recombinant enzyme was found to be a tetramer with each subunit having molecular weight of 50,000.