Higher magnification lenses versus conventional lenses for evaluation of diabetic neuropathy by corneal in vivo confocal microscopy

We investigated the association of CDKAL1 (rs7754840 and rs7756992) and CDKN2A/2B (rs10811661) variants with T2DM. Higher MAF of rs7754840 and rs7756992 were seen in patients, and both were associated with T2DM under additive, dominant, and recessive models. CDKAL1 rs7754840 and rs7756992, but not CDKN2A/2B rs10811661, are associated with T2DM in Lebanese.     

The origin and evolution of fragrance in rice (Oryza sativa L.)

Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (BADH2) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the BADH2 gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the badh2.1 allele within the Japonica varietal group and demonstrate the introgression of this allele from Japonica to Indica. Basmati-like accessions were nearly identical to the ancestral Japonica haplotype across a 5.3-Mb region flanking BADH2 regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the Japonica gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the Indica varietal group.     

Polymorphisms of MDR1, CYP2C19 and P2Y12 genes in Indian population: Effects on clopidogrel response

Aims/objectiveInfluence of genetic variations on the response of clopidogrel, an antiplatelet drug is implicated. In the present study, the prevalence of single nucleotide polymorphisms of MDR1 (C3435T), CYP2C19 [CYP2C19*2 CYP2C19*3, CYP2C19*17] and P2Y₁₂ (i-T744C) in Indian population and their effects on clopidogrel response was analyzed.Methods and resultsTo analyze the prevalence of polymorphisms, 102 healthy individuals were recruited. Clopidogrel response was assessed by ADP induced platelet aggregation in clopidogrel naïve acute myocardial infarction (AMI) patients (n = 26) screened from 100 AMI cases, before loading dose of 300 mg, at 24 h before next dose and 6 days after on 75 mg per day and platelet aggregation inhibition (PAI) was calculated between these time intervals. Genotyping was carried out by PCR-based restriction enzyme digestion method for C3435T of MDR1 and i-T744C of P2Y₁₂, by multiplex PCR for CYP2C19*2 (G681A) and CYP2C19*3 (G636A) and by nested PCR for CYP2C19*17 (C806T). The effect of the above mentioned genetic variations on PAI was analyzed. Variant allele of CYP2C19*3 was not observed while the prevalence of 3435T of MDR1 (0.524), CYP2C19*2 (681A, 0.352); i-744C of P2Y₁₂ (0.088), as well as wild type allele CYP2C19*17 (C806, 0.897) associated with decrease clopidogrel response were observed. Trend toward poor response to clopidogrel was observed at 24 h with the variant genotypes of CYP2C19*2 and i-T744C of P2Y₁₂ as compared to wild type.ConclusionThe present study did show a trend toward impaired response of clopidogrel to inhibit platelet aggregation with variant genotypes of CYP2C19*2 and iT744C of P2Y₁₂ compared to respective wild type genotype at 24 h.     

Synergistic effect of Bcl2, Myc and Ccnd1 transforms mouse primary B cells into malignant cells

Background

A synergistic effect resulting from a combination of BCL2 and MYC or MYC and CCND1 has been implicated in human B-cell lymphomas. Although the identification of other cooperative genes involved is important, our present understanding of such genes remains scant. The objective of this study was to identify the additional cooperative gene(s) associated with BCL2 and MYC or MYC and CCND1. First, we assessed whether Bcl2, Myc and Ccnd1 could cooperate. Next, we developed a synergism-based functional screening method for the identification of other oncogene(s) that act with Bcl2 and Myc.

Design and Methods

Growth in culture, colony formation and oncogenicity in vivo were assessed in mouse primary B cells exogenously expressing various combinations of Bcl2, Myc and Ccnd1. For the functional screening, Bcl2- and Myc-expressing primary B cells were infected with a retroviral cDNA library. Inserted cDNA of transformed cells in culture were then identified.

Results

Primary B cells exogenously expressing Bcl2, Myc and Ccnd1 showed factor-independent growth ability, enhanced colony-forming capability and aggressive oncogenicity, unlike the cases observed with the expression of any combination of only two of the genes. We identified CCND3 and NRAS as cooperative genes with Bcl2 and Myc through the functional screening.

Conclusions

Bcl2, Myc and Ccnd1 or Bcl2, Myc and CCND3 synergistically transformed mouse primary B cells into aggressive malignant cells. Our new synergism-based method is useful for the identification of synergistic gene combinations in tumor development, and may expand our systemic understanding of a wide range of cancer-causing elements.     

Association of Helicobacter pylori babA2 with peptic ulcer disease and gastric cancer

AIM: To investigate the association between babA2 gene and peptic ulcer disease (PUD) and gastric cancer (GC) in Helicobacter pylori -infected populations. METHODS: We evaluated the relationship between babA2 and clinical outcomes (PUD and GC) using a meta-analysis. A literature search was performed using the PubMed and Web of Science databases for relevant case-control studies that met the defined inclusion criteria. The ORs and 95%CIs were calculated to estimate the association between babA2 genotype and clinical outcomes. A fixed-effect or random-effect model was performed depending on the absence or presence of significant heterogeneity. RESULTS: A total of 25 articles with 38 studies met the inclusion criteria and were finally included in this metaanalysis. The results showed that the babA2 genotype was significantly associated with an increased risk of PUD (OR = 2.069, 95%CI: 1.530-2.794, P < 0.001) and especially in the subgroup of duodenal ulcer (OR = 1.588, 95%CI: 1.141-2.209, P = 0.006). Moreover, a significant association between babA2 gene and PUD and duodenal ulcer (OR = 2.739, 95%CI: 1.860-4.032, P < 0.001; OR = 2.239, 95%CI: 1.468-3.415, P < 0.001, respectively) was observed in western countries but not in Asian countries. CONCLUSION: We demonstrated that the presence of babA2 may be associated with increased risks for PUD, especially duodenal ulcer, in western countries.     

Comparative study of mutations in SNP loci of K-RAS,hMLH1 and hMSH2 genes in neoplastic intestinal polyps and colorectal cancer

AIM: To clarify the molecular mechanism involved in pathogenesis of colorectal cancer as well as clinical significance of genetic analysis of histological samples.METHODS: A total of 480 blood and tissue specimens were collected in our hospital from January 2011 to October 2012. In the observation group, there were 120 blood specimens and 120 intestinal tract tissue specimens collected from patients with neoplastic intestinal polyps. In the control group I there were 80 blood specimens and 80 intestinal tract tissue specimens collected from patients with colorectal cancer. In the control group II there were 40 blood specimens and 40 intestinal tract tissue specimens collected from healthy individuals. The gene segments were amplified using PCR and DNA gel electrophoresis along with DNA sequence analysis were employed for the detection of the following single nucleotide polymorphisms (SNPs): K-RAS codons 12 and 13; hMLH1 (human mutS homolog 1) gene missense mutation at Va1384Asp; hMSH2 (human mutS homolog 2) gene missense mutation at 2783C/A.RESULTS: The mutation rate of the SNP at Va1384Asp locus of the hMLH1 gene from blood and tissue specimens in the observation group showed no statistical difference from those in the control group I. The mutation rates of SNPs in codons 12 and 13 of K-RAS and at 2783C/A locus of the hMSH2 gene were significantly lower in the observation group than in the control group I (χ² = 15.476, 29.670, 10.811, 16.618, 33.538, 7.898, P < 0.05). The mutation rate of SNP at Va1384Asp locus of the hMLH1 gene was significantly higher in the observation group when compared to the control group II (χ² = 10.486, 4.876, P < 0.05). The mutation rates of SNPs in codons 12 and 13 of K-RAS and at 2783C/A locus of the hMSH2 gene did not show any statistical difference from those in the control group II.CONCLUSION: There may be important clinical significance and relevance between neoplastic intestinal polyps and colorectal cancer in terms of the mechanisms involved in the pathogenesis.     

Association between NOD2/CARD15 gene polymorphisms and Crohn’s disease in Chinese Zhuang patients

AIM:To assess the relationship between the P268S,JW1 and N852S polymorphisms and Crohn’s disease(CD)susceptibility in Zhuang patients in Guangxi,China.METHODS:Intestinal tissues from 102 Zhuang[48CD and 54 ulcerative colitis(UC)]and 100 Han(50 CD and 50 UC)unrelated patients with inflammatory bowel disease and 72 Zhuang and 78 Han unrelated healthy individuals were collected in the Guangxi Zhuang Autonomous Region from January 2009 to March 2013.Genomic DNA was extracted using the phenol chloroform method.The P268S,JW1 and N852S polymorphisms were amplified using polymerase chain reaction(PCR),detected by restriction fragment length polymorphism(RFLP),and verified by gene sequencing.RESULTS:Heterozygous mutation of P268S in the NOD2/CARD15 gene was detected in 10 CD cases(six Zhuang and four Han),two Han UC cases,and one Zhuang healthy control,and P268S was strongly associated with the Chinese Zhuang and Han CD populations(P=0.016 and 0.022,respectively).No homozygous mutant P268S was detected in any of the groups.No significant difference was found in P268S genotype and allele frequencies between UC and control groups(P>0.05).Patients with CD who carried P268S were likely to be≤40 years of age(P=0.040),but were not significantly different with regard to race,lesion site,complications,and other clinical features(P>0.05).Neither JW1 nor N852S polymorphisms of the NOD2/CARD15gene were found in any of the subjects(P>0.05).CONCLUSION:P268S polymorphism may be associated with CD susceptibility in the Zhuang population in the Guangxi Zhuang Autonomous Region,China.In contrast,JW1 and N852S polymorphisms may not be related to CD susceptibility in these patients.     

Mesenchymal-epithelial interactions involving epiregulin in tuberous sclerosis complex hamartomas

Patients with tuberous sclerosis complex (TSC) develop hamartomas containing biallelic inactivating mutations in either TSC1 or TSC2, resulting in mammalian target of rapamycin (mTOR) activation. Hamartomas overgrow epithelial and mesenchymal cells in TSC skin. The pathogenetic mechanisms for these changes had not been investigated, and the existence or location of cells with biallelic mutations ("two-hit" cells) was unclear. We compared TSC skin hamartomas (angiofibromas and periungual fibromas) with normal-appearing skin of the same patient, and we observed more proliferation and mTOR activation in hamartoma epidermis. Two-hit cells were not detected in the epidermis. Fibroblast-like cells in the dermis, however, exhibited allelic deletion of TSC2, in both touch preparations of fresh tumor samples and cells grown from TSC skin tumors, suggesting that increased epidermal proliferation and mTOR activation were not caused by second-hit mutations in the keratinocytes but by mesenchymal-epithelial interactions. Gene expression arrays, used to identify potential paracrine factors released by mesenchymal cells, revealed more epiregulin mRNA in fibroblast-like angiofibroma and periungual fibroma cells than in fibroblasts from normal-appearing skin of the same patient. Elevation of epiregulin mRNA was confirmed with real-time PCR, and increased amounts of epiregulin protein were demonstrated with immunoprecipitation. Epiregulin stimulated keratinocyte proliferation and phosphorylation of ribosomal protein S6 in vitro. These results suggest that hamartomatous TSC skin tumors are induced by paracrine factors released by two-hit cells in the dermis and that proliferation with mTOR activation of the overlying epidermis is an effect of epiregulin.     

From the Cover: Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass

DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3–Rev7–PolD2–PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3–Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3′ guanine and Pol ζ4 to extend the primers.DNA polymerase ζ (Pol ζ), composed of the catalytic Rev3 and accessary Rev7 subunits, is an error-prone DNA translesion polymerase that causes both spontaneous and DNA damage-induced mutagenesis (1, 2). More than two-thirds of the 1,504 residues in yeast Rev3 share sequence homology with all B-family DNA polymerases, including Pols α, δ, and ε, which are responsible for the bulk of high-fidelity genomic replication in eukaryotes (3). Unlike the typical B-family polymerases, Pol ζ lacks an intrinsic 3′–5′ exonuclease activity and thus has no proofreading function (2). Human homologs of REV3 (REV3L) and REV7 (MAD2L2; hereafter referred to as REV7) genes were identified shortly after yeast Pol ζ was characterized. Human Rev3 contains 3,130 residues and is twice as large as the yeast counterpart (4). Human and yeast Rev7 are homologous (5) and bear sequence similarity to the mitotic checkpoint proteins Mad2 (6). Unlike Saccharomyces cerevisiae REV3 and REV7 genes, which are nonessential and whose knockout leads only to a decreased rate of damage-induced mutagenesis (7, 8), Rev3l knockout in mice is embryonic-lethal (9), and mouse Rev3l^−/− embryonic stem cells are not viable (10, 11). Human and mouse cell cultures obtained from conditional Rev3l knockout show genome instability and growth defects without an external challenge of DNA damage (12–14). DNA pol ζ is apparently essential for normal cell proliferation and embryogenesis in mammals.Translesion synthesis (TLS) and DNA-damage-induced mutagenesis are the best-characterized functions of Pol ζ. Absence of the yeast REV3 gene leads to sensitivity to UV light and intrastrand and interstrand cross-linking agents (2, 15). DNA Pol ζ has been shown to induce multiple base substitutions as well as more complex mutations in yeast (7, 16, 17) and may contribute to hypermutation in Ig genes in mammals (18, 19). The TLS function of DNA Pol ζ has been implicated in its role of mediating resistance to platinum-based chemotherapies (20–22). Owing to the conservation of B-family DNA polymerases, a distorted DNA template base is unlikely to be accommodated in the active site of DNA Pol ζ. In fact, yeast DNA Pol ζ is unable to insert a nucleotide opposite either a cis–syn thymine or a 6-4 photoproduct (23). Genetic data indicate that a complete lesion bypass event may require two TLS DNA polymerases (24)—one for nucleotide incorporation opposite a lesion (insertion step) and the other for the subsequent primer extension (extension step). The insertion step of TLS is often accomplished by a Y-family polymerase, whose active site is uncommonly large, solvent-exposed, and flexible (25). Studies of another B-family TLS DNA polymerase from Escherichia coli (Pol II) show that it efficiently extends a DNA primer after a lesion by looping out the damaged DNA template strand, leading to frameshift and mixed-type mutations (26).In budding yeast, REV3 has been shown to be epistatic with POL32, a subunit of DNA Pol δ. Inactivating either REV3 or POL32 leads to reduced spontaneous mutagenesis (27–29). As with all eukaryotic B-family DNA polymerases, Rev3 contains a Cys-rich C-terminal domain (CTD) (30–33), which forms a zinc-finger domain followed by a [4Fe–4S] cluster (34). In Pol α, δ, and ε, each CTD interacts with its specific accessary subunits (32, 35). Recently, three groups have independently shown that the [4Fe–4S] cluster of yeast Rev3 interacts with Pol31 and Pol32 subunit (36), thus forming an stoichiometric four-subunit Pol ζ (Pol ζ4; Rev3–Rev7–Pol31–Pol32) (23, 37, 38). Baranovskiy et al. further showed that the CTDs of human Pol ζ and δ share the same accessary subunits p50 and p66, homologs of yeast Pol31 and Pol32, respectively (37). The interaction between yeast Rev3 and Pol31 is reported to be direct, and Pol32 is essential to stabilize Pol31 and, furthermore, via its interactions with proliferating cell nuclear antigen (PCNA), recruits and activates Pol ζ to carry out TLS (38). The catalytic activity of yeast Pol ζ is improved by the presence of Pol31 and Pol32 (23, 38).Purification and characterization of Pol ζ has so far been limited to the yeast protein. Perhaps because of its large size, mammalian Pol ζ has not been purified for biochemical characterization. To overcome this roadblock, we coexpressed human REV3L and REV7 in mammalian cells in culture. Initially, very low expression level and heterogeneity was encountered, but these problems were solved by targeted deletion of various internal segments of human REV3L. We succeeded in purifying an active two-subunit form of human Pol ζ (Pol ζ2). By differential pull-down experiments using Pol ζ2 variants with and without the CTD of Rev3, we isolated two CTD-dependent Pol ζ accessary subunits, PolD2 and PolD3. We report here purification of an active form of human four-subunit Pol ζ4 and the collaboration of two TLS polymerases, Pol η and Pol ζ, in lesion bypass.     

Control of seed mass and seed yield by the floral homeotic gene APETALA2

APETALA2 (AP2) is best known for its role in the regulation of flower meristem and flower organ identity and development in Arabidopsis. We show here that AP2 also plays an important role in determining seed size, seed weight, and the accumulation of seed oil and protein. We demonstrate genetically that AP2 acts through the maternal sporophyte and endosperm genomes to control seed weight and seed yield. Thus, AP2 functions outside the boundaries of flower meristem and flower organ development to affect agronomically relevant traits in Arabidopsis.     

PON2 and ATP2B2 gene polymorphisms with noise-induced hearing loss

Background

Noise-induced hearing loss (NIHL) is a complex disease induced by a combination of genetic and environmental factors. Paraoxonase2 (PON2) gene involved in the regulation of reactive oxygen species, and affecting the vulnerability of cochlea to NIHL, and ATPase, calcium-transporting, plasma membrane 2 (ATP2B2) gene which encodes plasma membrane calcium-transporting ATPase isoform 2 (PMCA2) are the candidate genes relating to the attack of NIHL. In this study, we investigated whether ATP2B2 and PON2 polymorphisms were associated with NIHL in Chinese of Han nationality population.

Methods

We performed a case-control study between six single nucleotide polymorphisms (SNPs) (rs1719571, rs3209637 and rs4327369 within ATP2B2, rs12026, rs7785846 and rs12704796 within PON2) and NIHL in 454 subjects. All the SNPs were genotypes, using the TaqMan MGB probe assay. Odds ratios (ORs) were calculated with 95% confidence intervals (95% CIs) with logistic regression analysis to test the level of association for SNPs.

Results

In our study, 221 subjects with hearing loss and 233 subjects without hearing loss were recruited. The frequencies of the CG and CG + GG genotype of rs12026 (PON2) conferred risk factors for NIHL with adjusted OR values of 2.62 (95% CI, 1.69–4.06) and 2.48 (95% CI, 1.63–3.78), respectively. This kind of significance was also found at locus rs7785846, where genotypes CT and CT + TT were the risk types, with adjusted ORs of 2.52 (95% CI, 1.62–3.93) and 2.35 (95% CI, 1.54–3.58), respectively. We performed stratified analysis per noise exposure level, when it came to rs7785846 and rs12026 in the >92 dB(A) noise exposure group, the subjects who carried heterozygote were of significantly (P<0.01) higher susceptibility to NIHL than homozygote carriers. By contrast, no significantly higher risk was found for any rs12704796 genotypes or any genotypes in ATP2B2 (P>0.05), which may suggest that these SNPs did not have significant effects on noise susceptibility across noise exposure.

Conclusions

Our research suggested that PON2 might play a role in the etiology of NIHL in Chinese of Han nationality population.     

Oscillations in extracellular pH and reactive oxygen species modulate tip growth of Arabidopsis root hairs

Root hairs show highly localized cell expansion focused to their growing tips. This growth pattern is accomplished through restriction of secretion to the elongating apex and modulation of cell wall properties, with the wall just behind the tip becoming rigidified to resist the lateral expansive forces of turgor. In this report we show that root hairs exhibit oscillating growth that is associated with oscillating increases in extracellular pH and reactive oxygen species (ROS), which lag growth by ≈7 s. Consistent with a role for these changes in growth control, artificially increasing extracellular pH arrested root hair elongation, whereas decreasing pH elicited bursting at the tip. Similarly, application of exogenous ROS arrested elongation, whereas scavenging of ROS led to root hair bursting. Roots hairs of the root hair-defective rhd2-1 mutant, which lack a functional version of the NADPH oxidase ATRBOH C, burst at the transition to tip growth. This phenotype could be rescued by elevating the pH of the growth medium to ≥6.0. Such rescued root hairs showed reduced cytoplasmic ROS levels and a lack of the oscillatory production of ROS at the tip. However, they exhibited apparently normal tip growth, including generation of the tip-focused Ca²⁺ gradient thought to drive apical growth, indicating that ATRBOH C is not absolutely required to sustain tip growth. These observations indicate that root hair elongation is coupled to spatially distinct regulation of extracellular pH and ROS production that likely affect wall properties associated with the polarized expansion of the cell.     

Glucose and fat metabolism in adipose tissue of acetyl-CoA carboxylase 2 knockout mice

Acc2-/- mutant mice, when fed a high-fat/high-carbohydrate (HF/HC) diet, were protected against diet-induced obesity and diabetes. To investigate the role of acetyl-CoA carboxylase 2 (ACC2) in the regulation of energy metabolism in adipose tissues, we studied fatty acid and glucose oxidation in primary cultures of adipocytes isolated from wild-type and Acc2-/- mutant mice fed either normal chow or a HF/HC diet. When fed normal chow, oxidation of [14C]palmitate in adipocytes of Acc2-/- mutant mice was approximately 80% higher than in adipocytes of WT mice, and it remained significantly higher in the presence of insulin. Interestingly, in addition to increased fatty acid oxidation, we also observed increased glucose oxidation in adipocytes of Acc2-/- mutant mice compared with that of WT mice. When fed a HF/HC diet for 4-5 months, adipocytes of Acc2-/- mutant mice maintained a 25% higher palmitate oxidation and a 2-fold higher glucose oxidation than WT mice. The mRNA level of glucose transporter 4 (GLUT4) decreased several fold in the adipose tissue of WT mice fed a HF/HC diet; however, in the adipose tissue of Acc2-/- mutant mice, it was 7-fold higher. Moreover, lipolysis activity was higher in adipocytes of Acc2-/- mutant mice compared with that in WT mice. These findings suggest that continuous fatty acid oxidation in the adipocytes of Acc2-/- mutant mice, combined with a higher level of glucose oxidation and a higher rate of lipolysis, are major factors leading to efficient maintenance of insulin sensitivity and leaner Acc2-/- mutant mice.     

Birth of a new gene on the Y chromosome of Drosophila melanogaster

Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.The mammalian Y chromosome has the lowest gene density of any chromosome, and most of its genes have a homolog on the X. This pattern is consistent with the mammalian sex chromosomes having originated from an ordinary pair of chromosomes, followed by massive gene loss from the Y (1–4). In contrast, the closest homologs of all Drosophila melanogaster Y-linked protein-encoding genes are autosomal, strongly suggesting that its Y chromosome has been acquiring genes from the autosomes (5–7). Indeed, gene gains, and not gene losses, have played the major role in shaping the gene content of the Drosophila Y, at least in the last ∼63 million years (My) (8, 9). Hence, the Drosophila Y chromosome seems to be evolving noncanonically (10) and is an ideal model to investigate the dynamics of gene gain on a nonrecombining Y chromosome.The Drosophila Y chromosome has long been known to contain genes essential for male fertility (11, 12). Due to its heterochromatic state, progress in the molecular identification of the Y-linked single-copy genes has been slow. male fertility factor kl5 (kl-5), the first single-copy gene identified, was found serendipitously; it encodes a motor protein (dynein heavy chain) required for flagellar beating (13). More recently, a combination of computational and experimental methods identified 11 single-copy Y-linked genes among the unmapped sequence scaffolds produced by the Drosophila Genome Project (5–7). These genes have two striking features: (i) their closest paralogs are autosomal and not X linked, and (ii) they have male-specific functions, such as the beating of sperm flagella reported for the kl-5 gene (14). The most likely explanation for this pattern is that Y-linked genes were acquired from the autosomes and have been retained because they confer a specific fitness advantage to their carriers. An autosomal origin has previously been reported for a few Y-linked genes in humans and a repetitive gene on the Drosophila Y (4, 15). However, unequivocal evidence of the autosomal origin of Drosophila Y-linked genes, and of the specific mechanism that originated them, is lacking due to their antiquity. The 11 known single-copy genes (kl-2, kl-3, kl-5, ARY, WDY, PRY, Pp1-Y1, Pp1-Y2, Ppr-Y, ORY, and CCY) represent ancient duplications, with amino acid identities to the putative ancestors ranging from 30% to 74%, and poor (if any) alignment at the nucleotide level. Most of them have introns in conserved positions compared with their autosomal paralogs, ruling out retrotransposition and suggesting DNA-based duplication as the mechanism. The original size of these putative duplications is unknown, because the similarity between autosomal and Y-linked regions is restricted to one gene in each case. Flanking sequences and contiguous genes either were not duplicated or were subsequently mutated and deleted beyond recognition.Here we describe flagrante delicto Y (FDY), a single copy Y-linked gene present only in D. melanogaster, and which is 98% identical at the nucleotide level to the autosomal gene vig2. Because its origin is very recent (it occurred after the split between D. melanogaster and Drosophila simulans, ∼4 Mya), it was possible to demonstrate that FDY arose from a DNA-based duplication of chromosome 3R to the Y: the duplicated segment spans 11 kb of autosomal sequence and includes five contiguous genes (vig2, Mocs2, CG42503, Clbn, and Bili); the last four genes became pseudogenes by rapid accumulation of deletions, point mutations, and transposable element insertions or by lack of expression. Thus, FDY unequivocally demonstrates that the Drosophila Y has acquired genes from autosomes. Several Y-linked genes such as kl-2, kl-3, and PRY are shared by distant Drosophila species that diverged ∼60 Mya, implying ancient acquisitions. FDY dates the more recent acquisition to ∼2 My, and hence strongly suggests that Drosophila Y has been continuously acquiring autosomal genes.     

Differential expression of pancreatic protein and chemosensing receptor m RNAs in NKCC1-null intestine

AIM: To investigate the intestinal functions of the NKCC1 Na~+-K~+-2Cl cotransporter(SLC12a2 gene), differential m RNA expression changes in NKCC1-null intestine were analyzed.METHODS: Microarray analysis of m RNA from intestines of adult wild-type mice and gene-targeted NKCC1-null mice(n = 6 of each genotype) was performed to identify patterns of differential gene expression changes. Differential expression patterns were further examined by Gene Ontology analysis using the online Gorilla program, and expression changes of selected genes were verified using northern blot analysis and quantitative real time-polymerase chain reaction. Histological staining and immunofluorescence were performed to identify cell types in which upregulated pancreatic digestive enzymes were expressed.RESULTS: Genes typically associated with pancreatic function were upregulated. These included lipase, amylase, elastase, and serine proteases indicative of pancreatic exocrine function, as well as insulin and regenerating islet genes, representative of endocrine function. Northern blot analysis and immunohistochemistry showed that differential expression of exocrine pancreas m RNAs was specific to the duodenum and localized to a subset of goblet cells. In addition, a major pattern of changes involving differential expression of olfactory receptors that function in chemical sensing, as well as other chemosensing G-protein coupled receptors, was observed. These changes in chemosensory receptor expression may be related to the failure of intestinal function and dependency on parenteral nutrition observed in humans with SLC12a2 mutations. CONCLUSION: The results suggest that loss of NKCC1 affects not only secretion, but also goblet cell function and chemosensing of intestinal contents via G-protein coupled chemosensory receptors.     

Clinicopathological features of lymphoma/leukemia patients carrying both BCL2 and MYC translocations

Background

Lymphoid neoplasm with 18q21.3/BCL2 and 8q24/MYC translocation to immunoglobulin (IG) genes as dual-hit lymphoma/leukemia is very rare and known to have a poor clinical outcome.

Design and Methods

To clarify the clinicopathological characteristics of this malignancy, we analyzed 27 cases of cytogenetically proven dual-hit lymphoma/leukemia.

Results

Dual-hit lymphoma/leukemia was diagnosed at presentation in 22 cases and at relapse or disease progression in 5 cases. At the time of diagnosis of dual-hit lymphoma/leukemia, extranodal involvement was found in 25 cases (93%) and central nervous system involvement occurred in 15 cases (56%). The median survival and 1-year survival rate of the 27 cases were only 6 months and 22%, respectively, after diagnosis of the dual-hit lymphoma/leukemia. Seven cases of triple-hit lymphoma/leukemia (dual-hit lymphoma/leukemia with 3q27/BCL6 translocation) were included; the median survival of these patients was only 4 months from the diagnosis of the dual-hit lymphoma/leukemia. The duration of survival of the patients with a triple-hit malignancy was shorter than that of the other 20 cases of dual-hit lymphoma/leukemia (p=0.02). The translocation partner of MYC subdivided the dual-hit cases into two groups; 14 cases of IGH and 13 cases of IGK/L. The MIB-1 index was investigated in 14 cases with aggressive B-cell lymphoma, and was higher in the group with MYC-IGH translocation (n=7) than in the MYC-IGK/L group (n=7) (p=0.02). Overall survival was not different between the MYC-IGH translocation group (n=14) and the MYC-IGK or MYC-IGL translocation group (n=13).

Conclusions

Dual-hit lymphoma/leukemia is a rare but distinct mature B-cell neoplasm with an extremely poor prognosis characterized by frequent extranodal involvement and central nervous system progression with either of the translocation partners of MYC.