Multiple products of the Drosophila Shaker gene may contribute to potassium channel diversity

K+ channels are known through electrophysiology and pharmacology to be an exceptionally diverse group of channels. Molecular studies of the Shaker (Sh) locus in Drosophila have provided the first glimpse of K+ channel structure. The sequences of several Sh cDNA clones have been reported; none are identical. We have isolated and examined 18 additional Sh cDNAs in an attempt to understand the origin, extent, and significance of the variability. The diversity is extensive: we have already identified cDNAs representing at least nine distinct types, and Sh could potentially encode 24 or more products. This diversity, however, fits a simple pattern in which variable 3' and 5' ends are spliced onto a central constant region to yield different cDNA types. These different Sh cDNAs encode proteins with distinct structural features.     

Anthropogenic noise decreases urban songbird diversity and may contribute to homogenization

More humans reside in urban areas than at any other time in history. Protected urban green spaces and transportation greenbelts support many species, but diversity in these areas is generally lower than in undeveloped landscapes. Habitat degradation and fragmentation contribute to lowered diversity and urban homogenization, but less is known about the role of anthropogenic noise. Songbirds are especially vulnerable to anthropogenic noise because they rely on acoustic signals for communication. Recent studies suggest that anthropogenic noise reduces the density and reproductive success of some bird species, but that species which vocalize at frequencies above those of anthropogenic noise are more likely to inhabit noisy areas. We hypothesize that anthropogenic noise is contributing to declines in urban diversity by reducing the abundance of select species in noisy areas, and that species with low‐frequency songs are those most likely to be affected. To examine this relationship, we calculated the noise‐associated change in overall species richness and in abundance for seven common songbird species. After accounting for variance due to vegetative differences, species richness and the abundance of three of seven species were reduced in noisier locations. Acoustic analysis revealed that minimum song frequency was highly predictive of a species' response to noise, with lower minimum song frequencies incurring greater noise‐associated reduction in abundance. These results suggest that anthropogenic noise affects some species independently of vegetative conditions, exacerbating the exclusion of some songbird species in otherwise suitable habitat. Minimum song frequency may provide a useful metric to predict how particular species will be affected by noise. In sum, mitigation of noise may enhance habitat suitability for many songbird species, especially for species with songs that include low‐frequency elements.     

Replication-associated purine asymmetry may contribute to strand-biased gene distribution

Among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. Several hypotheses explaining this strand-biased gene distribution (SGD) have been proposed, but none have been tested or supported by sufficient data analyses. In this work we have analyzed 211 prokaryotic genomes in terms of compositional strand asymmetries and the presence or absence of polC and have found that SGD correlates not only with polC, but also with purine asymmetry (PAS). Furthermore, SGD, PAS, and polC are all features associated with a group of low-GC, gram-positive bacteria (Firmicutes). We conclude that PAS is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC and dnaE, which may play a direct role in the maintenance of SGD.     

Limb bud and flank mesoderm have distinct "physical phenotypes" that may contribute to limb budding

Limb bud outgrowth in chicken embryos is initiated during the third day of development by Fibroblast Growth Factor 8 (FGF8) produced by the newly formed apical ectodermal ridge (AER). One of the earliest effects of this induction is a change in the properties of the limb field mesoderm leading to bulging of the limb buds from the body wall. Heintzelman et al. [Heintzelman, K.F., Phillips, H.M., Davis, G.S., 1978. Liquid-tissue behavior and differential cohesiveness during chick limb budding. J. Embryol. Exp. Morphol. 47, 1–15.] suggested that budding of the limbs is caused by a higher liquid-like cohesivity of limb bud tissue compared with flank. We sought additional evidence relevant to this hypothesis by performing direct measurements of the effective surface tension, a measure of relative tissue cohesivity, of 4-day embryonic chicken wing and leg bud mesenchymal tissue, and adjacent flank mesoderm. As predicted, the two types of limb tissues were 1.5- to 2-fold more cohesive than the flank tissue. These differences paralleled cell number and volume density differences: 4-day limb buds had 2- to 2.5-fold as many cells per unit area of tissue as surrounding flank, a difference also seen at 3 days, when limb budding begins. Exposure of flank tissue to exogenous FGF8 for 24 h increased its cell number and raised its cohesivity to limb-like values. Four-day flank tissue exhibited a novel and unique active rebound response to compression, which was suppressed by the drug latrunculin and therefore dependent on an intact actin cytoskeleton. Correspondingly, flank at this stage expressed high levels of α-smooth muscle actin (SMA) mRNA and protein and a dense network of microfilaments. Treatment of flank with FGF8 eliminated the rebound response. We term material properties of tissues, such as cohesivity and mechanical excitability, the “physical phenotype”, and propose that changes thereof are driving forces of morphogenesis. Our results indicate that two independent aspects of the physical phenotype of flank mesoderm can be converted to a limb-like state in response to treatment with FGF8. The higher tissue cohesivity induced by this effect will cause the incipient limb bud to phase separate from the surrounding flank, while the active mechanical response of the flank could help ensure that the limb bud bulges out from, rather than becoming engulfed by, this less cohesive tissue.     

The Eb beta gene may have acted as the donor gene in a gene conversion-like event generating the Abm 12 beta mutant

At least two different class II histocompatibility antigens, I-A and I-E, are encoded by the murine major histocompatibility complex. Both types of class II antigens are composed of polypeptide chains called alpha and beta. Class II antigens display extensive genetic polymorphism, the main part of which resides in the NH2-terminal domains of the A alpha, A beta and E beta chains. Recently it was shown that the mutant gene Abm 12 beta differed from the wild-type gene Ab beta by three nucleotide substitutions, which all occur within a stretch of 14 nucleotides. Multiple substitutions of the type found in the Abm 12 beta gene suggest that the mutant arose by a gene conversion-like event. To examine whether the Eb beta gene may have served as the donor gene in the generation of the Abm 12 beta gene, we have isolated and sequenced a cDNA clone corresponding to the Eb beta gene. Comparisons of the Eb beta, the Ab beta and the Abm 12 beta nucleotide sequences revealed that the Eb beta sequence is identical to that of Abm 12 beta in the positions where the latter differs from the Ab beta sequence. This observation is consistent with the notion that the Abm 12 beta mutant gene arose by a gene conversion-like event involving the Eb beta gene.     

Recombination events suggest potential sites for the Huntington's disease gene

The Huntington's disease gene (HD) maps distal to the D4S10 marker in the terminal 4p16.3 subband of chromosome 4. Directed cloning has provided several DNA segments that have been grouped into three clusters on a physical map of approximately 5 X 10(6) bp in 4p16.3. We have typed RFLPs in both reference and HD pedigrees to produce a fine-structure genetic map that establishes the relative order of the clusters and further narrows the target area containing the HD gene. Despite the large number of meiotic events examined, the HD gene cannot be positioned relative to the most distal cluster. One recombination event with HD suggests that the terminal-most markers flank the disease gene; two others favor a telomeric location for the defect. Efforts to isolate the HD gene must be divided between these two distinct intervals until additional genetic data resolve the apparent contradiction in localization.     

Recombination events in Neurospora crassa may cross a translocation breakpoint by a template-switching mechanism

To assist investigation of the effect of sequence heterology on recombination in Neurospora crassa, we inserted the Herpes simplex thymidine kinase gene (TK) as an unselected marker on linkage group I, giving a gene order of Cen-his-3-TK-cog-lpl. We show here that in crosses heterozygous for TK, conversion of a his-3 allele on one homolog is accompanied by transfer of the heterologous sequence between cog and his-3 from the other homolog, indicating that recombination is initiated centromere-distal of TK. We have identified a 10-nucleotide motif in the cog region that, although unlikely to be sufficient for hotspot activity, is required for high-frequency recombination and, because conversion of silent sequence markers declines on either side, may be the recombination initiation site. Additionally, we have mapped conversion tracts in His(+) progeny of a translocation heterozygote, in which the translocation breakpoint separates cog from the 5' end of his-3. We present molecular evidence of recombination on both sides of the breakpoint. Because recombination is initiated close to cog and the event must therefore cross the translocation breakpoint, we suggest that template switching occurs in some recombination events, with repair synthesis alternating between use of the homolog and the initiating chromatid as template.     

A novel mutation in the connexin 29 gene may contribute to nonsyndromic hearing loss

Connexins (Cxs) are homologous four-transmembrane domain proteins and constitute the major components of gap junctions. Among a cohort of patients with nonsyndromic hearing loss, we recently identified a novel missense mutation, E269D, in the GJC3 gene encoding connexin 29 (Cx29), as being causally related to hearing loss. The functional alteration of Cx29 caused by the mutant GJC3 gene, however, remains unknown. This study compared the intracellular distribution and assembly of mutant Cx29 (Cx29E269D) with that of the wild-type Cx29 (Cx29WT) in HeLa cells and the effect the mutant protein had on those cells. Cx29TW showed continuous staining along apposed cell membranes in the fluorescent localization assay. In contrast, the p.E269D missense mutation resulted in accumulation of the Cx29 mutant protein in the endoplasmic reticulum (ER) rather than in the cytoplasmic membrane. Co-expression of Cx29WT and Cx29E269D proteins by a bi-directional tet-on expression system demonstrated that the heteromeric connexon accumulated in the cytoplasm, thereby impairing the formation of the gap junction. Based on these findings, we suggest that Cx29E269D has a dominant negative effect on the formation and function of the gap junction. These results provide a novel molecular explanation for the role Cx29 plays in the development of hearing loss.     

Extensive polymorphism of ABO blood group gene: three major lineages of the alleles for the common ABO phenotypes

Polymorphism of the ABO blood group gene was investigated in 262 healthy Japanese donors by a polymerase chain reactions-single-strand conformation polymorphism (PCR-SSCP) method, and 13 different alleles were identified. The number of alleles identified in each group was 4 for A¹ (provisionally called ABO*A101, *A102, *A103 and *A104 according to the guidelines for human gene nomenclature), 3 for B (ABO*B101, *B102 and *B103), and 6 for O (ABO*O101, *O102, *O103, *O201, *O202 and *O203). Nucleotide sequences of the amplified fragments with different SSCP patterns were determined by direct sequencing. Phylogenetic network analysis revealed that these alleles could be classified into three major lineages, *A/*O1, *B and *O2. In Japanese, *A102 and *13101 were the predominant alleles with frequencies of 83% and 97% in each group, respectively, whereas in group O, two common alleles, *O101 (43%) and *O201 (53%), were observed. These results may be useful for the establishment of ABO genotyping, and these newly described ABO alleles would be advantageous indicators for population studies.     

TCRJ and BCRJ gene segments contain 5′ D-segment sequences that contribute to repertoire diversity

T cell receptor (TCR) and B cell receptors (BCR) junctions, also known as the CDR3, are where the V, D, and J gene segments converge, coding for a loop structure important for contacting ligands. J segments contribute to the formation of the CDR3 loop through their 5′ ends that vary in length and show high sequence variability. The 5′ ends of J segments of TCRα genes show nucleotide sequence similarities to TCRDδ segments as high as 89% and show a preponderance of murine TCRDδ2 or human TCRDδ3 amino acid sequence similarities. Surprisingly, most of the 5′ ends of TCRJγ segments show nucleotide and amino acid sequence similarities with TCRDβ segments. All murine and human BCRJH segments and most TCRJδ segments contain amino acid sequences at their 5′ ends that resemble their own D segments, a finding that is not seen with TCRJβ segments. TCRα and TCRγ genes thus make up for their lack of separate D segments with distinct D-like segments that are built into the 5′ ends of their J segments. Additionally, in some cases, TCR and BCR genes that utilize separate D segments also receive additional D-like contributions though the 5′ ends of their J segments to add additional diversity to their CDR3 loops.     

Genetic variations in the KIR gene family may contribute to susceptibility to ankylosing spondylitis: a meta-analysis

The present meta-analysis of relevant case–control studies was conducted to investigate the possible relationships between genetic variations in the killer cell immunoglobulin-like receptor (KIR) gene clusters of the human KIR gene family and susceptibility to ankylosing spondylitis (AS). The following electronic databases were searched for relevant articles without language restrictions: the Web of Science, the Cochrane Library Database, PubMed, EMBASE, CINAHL, the Chinese Biomedical Database (CBM) and Chinese National Knowledge Infrastructure (CNKI) databases, covering all papers published until 2013. STATA statistical software was adopted in this meta-analysis as well. We also calculated the crude odds ratios (OR) and its 95 % confidence intervals (95 % CI). Seven case–control studies with 1,004 patients diagnosed with AS and 2,138 healthy cases were implicated in our meta-analysis, and 15 genes in the KIR gene family were also evaluated. The results of our meta-analysis show statistical significance between the genetic variations in the KIR2DL1, KIR2DS4, KIR2DS5 and KIR3DS1 genes and an increased susceptibility to AS (KIR2DL1: OR 7.82, 95 % CI 3.87–15.81, P< 0.001; KIR2DS4: OR 1.91, 95 % CI 1.16–3.13, P = 0.010; KIR2DS5: OR1.51, 95 % CI 1.14–2.01, P = 0.004; KIR3DS1: OR 1.58, 95 % CI 1.34–1.86, P< 0.001; respectively). However, we failed to found positive correlations between other genes and susceptibility to AS (all P >0.05). The current meta-analysis provides reliable evidence that genetic variations in the KIR gene family may contribute to susceptibility to AS, especially for the KIR2DL1, KIR2DS4, KIR2DS5 and KIR3DS1 genes.     

Molecular cloning and functional expression of KCNQ5, a potassium channel subunit that may contribute to neuronal M-current diversity

We have isolated KCNQ5, a novel human member of the KCNQ potassium channel gene family that is differentially expressed in subregions of the brain and in skeletal muscle. When expressed in Xenopus oocytes, KCNQ5 generated voltage-dependent, slowly activating K(+)-selective currents that displayed a marked inward rectification at positive membrane voltages. KCNQ5 currents were insensitive to the K(+) channel blocker tetraethylammonium but were strongly inhibited by the selective M-current blocker linopirdine. Upon coexpression with the structurally related KCNQ3 channel subunit, current amplitudes increased 4-5-fold. Compared with homomeric KCNQ5 currents, KCNQ3/KCNQ5 currents also displayed slower activation kinetics and less inward rectification, indicating that KCNQ5 combined with KCNQ3 to form functional heteromeric channel proteins. This functional interaction between KCNQ5 and KCNQ3, a component of the M-channel, suggests that KCNQ5 may contribute to a diversity of heteromeric channels underlying native neuronal M-currents.     

Molecular mimicry may contribute to pathogenesis of ulcerative colitis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease with mucosal inflammation and ulceration of the colon. There seems to be no single etiological factor responsible for the onset of the disease. Autoimmunity has been emphasized in the pathogenesis of UC. Perinuclear anti-neutrophil cytoplasmic antibodies (pANCA) are common in UC, and recently two major species of proteins immunoreactive to pANCA were detected in bacteria from the anaerobic libraries. This implicates colonic bacterial protein as a possible trigger for the disease-associated immune response. Autoantibodies and T-cell response against human tropomyosin isoform 5 (hTM5), an isoform predominantly expressed in colon epithelial cells, were demonstrated in patients with UC but not in Crohn's colitis. We identified two bacterial protein sequences in NCBI database that have regions of significant sequence homology with hTM5. Our hypothesis is that molecular mimicry may be responsible for the pathogenesis of UC.     

Free radicals may contribute to oxidative skeletal muscle fatigue

We used mouse soleus in vitro (n = 30) and canine gastrocnemius-plantaris preparations (n = 20) pump-perfused at the animal's blood pressure to establish if free radicals contribute to fatigue in oxidative skeletal muscle. The soleus from each leg contracted for 200 ms (70 Hz) once every minute for 60 min in Hepes buffer gassed with 100% oxygen at 27 degrees C. When contracting in Hepes alone, both muscles fatigued at 0.9 mN/mm2.min over the 60 min. The addition of purines to the bath increased the rate to 1.4 mN/mm2.min and the addition of xanthine oxidase to generate free radicals increased the rate again to 1.9 mN/mm2.min. Thus free radicals appeared to attenuate oxidative skeletal muscle function. Each canine muscle contracted isometrically at 4 Hz for 30 min and then rested for 45 min before contracting for a second 30 min at 4 Hz. In each experiment, we infused saline at 0.76 mL/min into resting muscle and at 1.91 mL/min during the first contraction period. During the remainder of the experiment, we infused, at the same rates, saline (n = 4), 10 microM dimethyl sulfoxide (DMSO) (n = 4) to identify the effect of scavenging hydroxyl radicals, 1 mM allopurinol to establish the effect of blocking xanthine oxidase (n = 4), or 200 microM desferoxamine to determine the effect of chelating iron (n = 4). With saline, the fatigue rate over the 30 min of contractions increased from 5.0 +/- 0.2 to 6.3 +/- 0.5 N/kg.min from the first to the second stimulation period. The fatigue rate was slower in the second period with each of the three experimental substances (DMSO, 5.9 +/- 0.8 to 3.2 +/- 0.3; allopurinol, 7.3 +/- 1.1 to 4.6 +/- 0.6; desferoxamine, 6.8 +/- 0.8 to 4.4 +/- 0.8 N/kg.min). The fatigue rate was the same as control when DMSO was infused only during the second contraction period. Therefore, free radicals appeared to contribute to fatigue in oxidative skeletal muscle.