Genetic interactions suggest that Danforth's short tail (Sd) is a gain-of-function mutation

Danforth's short tail (Sd) is a semidominant mutation on mouse chromosome 2 that acts cell autonomously in the notochord and leads to its disintegration, and thus causes severe defects in somite patterning and vertebral column development. The molecular nature of the Sd gene and mutation is unknown, and it is unclear whether Sd is a loss-of-function mutation and the semidominant inheritance of the Sd phenotype is due to haploinsufficiency, or whether Sd represents a gain-of-function mutation in a gene essential for notochord development and maintenance. Here, we report on the genetic interaction between Sd and an insertional mutation called Etl4^lacZ, which provides genetic evidence that Sd is a gain-of-function mutation. Etl4^lacZ is an enhancer trap insertion, which gives rise to lacZ expression in distinct cell types, including the notochord. In homozygosity, the lacZ insertion leads to abnormal vertebrae in the caudal part of the vertebral column. Etl4^lacZ maps approximately 0.75 cM distal to Sd, and in double heterozygotes modifies the Sdphenotype contrarily, depending on the chromosomal configuration of the Sd and Etl4^lacZ mutations: when Etl4^lacZ is present on the chromosome wild type for Sd (Sd +/+ Etl4^lacZ; trans configuration), the Sd phenotype is enhanced, i.e., vertebral malformations extend to more anterior positions and the vertebral body of the axis is further reduced. Conversely, when Etl4^lacZ is present on the same chromosome as Sd (Sd Etl4^lacZ /+ +; cis configuration), the Sd phenotype is attenuated, i.e., vertebral malformations are confined to more posterior levels, and the dens axis, which is severely reduced or absent in Sd heterozygotes, is restored. The different effect of the Etl4^lacZ insertion on Sd, depending on its presence in trans or cis, suggests a direct interaction of the transgene insertion with the Sd gene. Additionally, the attenuation of the Sd phenotype by Etl4^lacZ in cis suggests that Sd is a gain-of-function mutation and lends support to the idea that Etl4^lacZ is a new allele of Sd. Dev. Genet. 23:86–96, 1998. © 1998 Wiley-Liss, Inc.     

Oenothera mitochondrial orf454, a gene involved in cytochrome c biogenesis corresponds to orf169 and orf322 of Marchantia

We have characterized a mitochondrial gene in Oenothera, designated orf454, capable of encoding a component of the cytochrome c biogenesis system. This open reading frame is interrupted by an intron of 941 nucleotides showing high similarity to a group II intron residing in the rpl2 gene. RNA editing, which is observed at 18 cytidine positions within the orf454 reading frame, improves the similarity to protein-coding sequences in bacteria and higher plants and removes the last 16 amino acids. orf454 also shows high sequence similarity to two overlapping reading frames (orf169 and orf322) of Marchantia mitochondria. These ORFs belong to an operon-like cluster of genes in the liverwort that is not conserved in Oenothera mitochondria. However, in bacteria these reading frames are organized like the Marchantia gene cluster. It has been shown by genetical analysis in Rhodobacter capsulatus that these genes are essential for cytochrome c biogenesis. Genes of bacterial operons — ccl1 in Rhodobacter and yejR and nrfE in Escherichia coli — show high sequence similarity to the mitochondrial reading frames orf577 and orf454 of Oenothera. orf454, which we describe here, is homologous to the C-terminal region of these bacterial genes, while the previously described orf577 is homologous to the N-terminal region.     

Inflorescence development in the Vitis–Ampelocissus clade of Vitaceae: the unusual lamellate inflorescence of Pterisanthes

Pterisanthes (Vitaceae) is a genus of c. 20 species of scandent climbers endemic to Southeast Asia with unusual lamellate inflorescences. Molecular phylogenetic analysis supports its relationship in the well‐supported Vitis–Ampelocissus–Nothocissus–Pterisanthes clade (i.e. the Ampelocissus–Vitis clade). Shoot tips and floral buds were collected from wild and greenhouse‐grown P. eriopoda at different developmental stages and were examined using epi‐illumination, light and scanning electron microscopy. Inflorescence and floral ontogeny was studied to discover how the lamellate inflorescence evolved and to make morphological comparisons to infer relationships with closely related members of Vitaceae. The second‐order branches in P. eriopoda are racemose and develop helically around the inflorescence axis in a similar fashion to Vitis and Ampelocissus. Inflorescence branching is restricted to the second order in P. eriopoda, whereas in Vitis and most Ampelocissus species subsequent branching orders culminate in the typical vitaceous determinate dichasium. In P. eriopoda subsequent lateral growth of the second‐order branches combined with the inhibition of peduncle or pedicel formation and loss of dichasial branching results in the unique lamellae in Pterisanthes, on which the floral primordia arise directly in a helical pattern. Floral development in P. eriopoda is the same as in other genera of Vitaceae examined to date with initiation of floral whorls centripetally, the calyx ring developing first and calyx lobes fused to cover the petals and stamen primordia. Given the recent phylogenetic results that placed Pterisanthes firmly within Ampelocissus, the most likely scenario is that the Pterisanthes inflorescence is derived from the thyrse of an Ampelocissus‐like ancestor and that the thyrse is a morphological synapomorphy of the Ampelocissus–Vitis clade. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 725–741.     

Molecular phylogeny of Macrolycus (Coleoptera: Lycidae) with description of new species from China

Macrolycus is a genus of net‐winged beetles with 69 species distributed in the eastern Palearctic and northernmost part of the Oriental region. The first molecular phylogeny of Macrolycus was produced using an rrnL + tRNA‐Leu + nad1 mtDNA fragment. The major lineages and species limits were identified with morphology and molecular data. We propose that Cerceros is a subgenus of Macrolycus to enable identification of all adult specimens in the genus without DNA sequencing. Two species groups are proposed in Macrolycus s. str. and six in Cerceros. Additionally, twelve Macrolycus species are newly described from China: M. aquilinus, M. baihualingensis, M. bicolor, M. guangxiensis, M. jianfenglingensis, M. kuatunensis, M. lizipingensis, M. parvus, M. phoeniceus, M. rhodoneurus, M. rosaceus and M. sichuanensis. Macrolycus holzschuhi is proposed to be a junior subjective synonym of M. jeanvoinei. The highest diversity of Macrolycus is found in southern China. The species from the main islands of Japan are placed in two species groups: M. excellens is a sister to remaining species of the M. murzini group and the M. flabellatus group is a monophylum of closely related species in a sister position to the M. bicolor group.     

Locus determining the human sperm-specific lactate dehydrogenase,LDHC, is syntenic with LDHC

From the data presented in this report, the human LDHC gene locus is assigned to chromosome 11. Three genes determine lactate dehydrogenase (LDH) in man. LDHA and LDHB are expressed in most somatic tissues, while expression of LDHC is confined to the germinal epithelium of the testes. A human LDHC cDNA clone was used as a probe to analyze genomic DNA from rodent/human somatic cell hybrids. The pattern of bands with LDHC hybridization is easily distinguished from the pattern detected by LDHA hybridization, and the LDHC probe is specific for testis mRNA. The structural gene LDHA has been previously assigned to human chromosome 11, while LDHB maps to chromosome 12. Studies of pigeon LDH have shown tight linkage between LDHB and LDHC leading to the expectation that these genes would be syntenic in man. However, the data presented in this paper show conclusively that LDHC is syntenic with LDHA on human chromosome 11. The terminology for LDH genes LDHA, LDHB, and LDHC is equivalent to Ldhl, Ldh2, and Ldh3, respectively.     

A complex genetic locus controlling purine nucleotide biosynthesis in yeast

Summary Mutants of the genes pur1 to pur6 excrete purine when in combination with the allele su-pur ⁺ and are resistant to growth inhibition by 8-azaadenine (8-AzAd) and 8-azaguanine (8-AzGu). In combination with su-pur, which suppresses purine excretion, pur1 and pur2 are analogue sensitive; pur3 is slightly resistant to 8-AzAd; pur4 is slightly resistant to both analogues and pur5 is completely resistant to 8-AzGu. Crosses of the pur mutants to dap, which causes sensitivity to 2,6-diaminopurine (2,6-DAP), guanine and 6-mercaptopurine (6-MP), show that dap also suppresses purine excretion and is closely linked to pur6. In combination with dap, pur1 and pur3 are analogue sensitive; pur4 is hypersensitive to guanine but resistant to 6-MP; pur5 is resistant to 2,6-DAP and guanine whilst pur2 is hypersensitive to all three compounds.The gene slw, which, like pur2, potentiates the effects of dap, also suppresses purine excretion but is not linked to any of the pur genes. The diploid slw/pur3 excretes purine.Tests for functional allelism were carried out on the closely linked genotypes su-pur ⁺, su-pur, dap, pur6, PUR6 and ade4. The results of these tests indicate that all six genotypes are functionally allelic. It is suggested that a molecular complex of the products of pur1, pur3, pur4, pur6 and slw is involved in the control of purine nucleotide biosynthesis in yeast.     

Electrostatic effects on polynucleotide transitions. II. Behavior of titrated systems

The theory developed in the previous paper to discuss changes in electrostatic free energies in polynucleotide order–disorder transitions is extended to cases where one or more of the participating species is titrated to some degree α. It is shown that, for any class of transition, the melting temperature T_m at constant pH is a linear function of the logarithm of the monovalent counterion concentration M, that at high salt the logarithm of the depression of the melting temperature by pH titration is proportional to the pH change, and that the stability of the ordered form as measured by its melting temperature at neutral pH, is a monotonic function of the quantity pH_m – pK, where pH_m and pK are the pH of melting and the monomer base pK, both measured under similar conditions of temperature and ionic strength. For the transition from double helix to coil, the dependences of T_m and dT_m/d log M on pH are determined experimentally and compared with the qualitative predictions of the theory. It is found that dT_m/dlog M, a measure of – ΔF?^el (the negative of the electrostatic free energy change in the transition), decreases with increasing pH. In acid solution, where the coil is more extensively prolonated than the helix, the change in electrostatic free energy in the transition is larger than at neutral pH. Conversely, in alkali the electrostatic five energy change is smaller than at neutral pH. Hence (dT_m/d log M)_acid > (dT_m/d log M _neutral) > (dT_m/d log M)_alkali. At Suffeciently high pH, dT_m/d log M is observed to become negative, indicating that the electrostatic free energy change is positive in the transition of this region. Date from the literature on the ionic strength dependence of the melting temperature for the acid helices of poly rA, poly rC, and poly dC are also considered from the standpoint of the theory.     

Temperature regulation of membrane composition in the Firmicute,Enterococcus faecalis,parallels that of Escherichia coli

Both Enterococcus faecalis and Escherichia coli can undergo abrupt temperature transitions in nature. E. coli changes the composition of its phospholipid acyl chains in response to shifts growth temperature. This is mediated by a naturally temperature sensitive enzyme, FabF (3-ketoacyl-acyl carrier protein synthase II), that elongates the 16 carbon unsaturated acyl chain palmitoleate to the 18 carbon unsaturated acyl chain, cis-vaccenate. FabF is more active at low temperatures resulting in increased incorporation of cis-vaccenoyl acyl chains into the membrane phospholipids. This response to temperature is an intrinsic property of FabF and does not require increased synthesis of the enzyme. We report that the FabF of the very divergent bacterium, E. faecalis, has properties very similar to E. coli FabF and is responsible for changing E. faecalis membrane phospholipid acyl chain composition in response to temperature. Moreover, expression E. faecalis FabF in an E. coli ∆fabF strain restores temperature regulation to the E. coli strain.     

Drift variances of FSTand GST statistics obtained from a finite number of isolated populations

Approximate formulas for the mean and variance of the F_STor G_ST statistic in a finite number of isolated populations are developed under the effect of random genetic drift. Computer simulation has shown that the approximate formulas give a fairly accurate result unless the initial frequency of one of the alleles involved is close to 1 and t/2N is large, where N is the effective size of a subpopulation and t is the number of generations. It is shown that when the number of subpopulations (s) is small, the mean of F_STor G_ST depends on the initial gene frequencies as well as on s. When the initial frequencies of all alleles are nearly equal to each other and the number of subpopulations is large, the distribution of F_ST in the early generations is bell-shaped. In this case Lewontin and Krakauer's k parameter is approximately 2 or less. However, if one of the initial allele frequencies is close to 1, the distribution is skewed and leptokurtic, and the k parameter often becomes larger than 2 in later generations. Thus, even under pure random genetic drift, Lewontin and Krakauer's test of selective neutrality of polymorphic genes in terms of F_ST is not always valid. It is also shown that Jacquard's approximate formula for k generally gives an overestimate.     

Distinct expression patterns for two Xenopus Bar homeobox genes

The BarH1 and BarH2 homeobox genes are coexpressed in cells of the fly retina and in the central and peripheral nervous systems. The fly Bar genes are required for normal development of the eye and external sensory organs. In Xenopus we have identified two distinct vertebrate Bar-related homeobox genes, XBH1 and XBH2. XBH1 is highly related in sequence and expression pattern to a mammalian gene, MBH1, suggesting that they are orthologues. XBH2 has not previously been identified but is clearly related to the Drosophila Bar genes. During early Xenopus embryogenesis XBH1 and XBH2 are expressed in overlapping regions of the central nervous system. XBH1, but not XBH2, is expressed in the developing retina. By comparing the expression of XBH1 with that of hermes, a marker of differentiated retinal ganglion cells, we show that XBH1 is expressed in retinal ganglion cells during the differentiation process, but is down-regulated as cells become terminally differentiated. Received: 12 August 1999 / Accepted: 5 October 1999     

On the Evolution of Dopa decarboxylase (Ddc) and Drosophila Systematics

We have sequenced most of the coding region of the gene Dopa decarboxylase (Ddc) in 24 fruitfly species. The Ddc gene is quite informative about Drosophila phylogeny. Several outstanding issues in Drosophila phylogeny are resolved by analysis of the Ddc sequences alone or in combination with three other genes, Sod, Adh, and Gpdh. The three species groups, melanogaster, obscura, and willistoni, are each monophyletic and all three combined form a monophyletic group, which corresponds to the subgenus Sophophora. The Sophophora subgenus is the sister group to all other Drosophila subgenera (including some named genera, previously considered outside the Drosophila genus, namely, Scaptomyza and Zaprionus, which are therefore downgraded to the category of subgenus). The Hawaiian Drosophila and Scaptomyza are a monophyletic group, which is the sister clade to the virilis and repleta groups of the subgenus Drosophila. The subgenus Drosophila appears to be paraphyletic, although this is not definitely resolved. The two genera Scaptodrosophila and Chymomyza are older than the genus Drosophila. The data favor the hypothesis that Chymomyza is older than Scaptodrosophila, although this issue is not definitely resolved. Molecular evolution is erratic. The rates of nucleotide substitution in 3rd codon position relative to positions 1 + 2 vary from one species lineage to another and from gene to gene. Received: 2 June 1998 / Accepted: 3 September 1998     

Inheritance and molecular mapping of new greenbug resistance genes in wheat germplasms derived from Aegilops tauschii

Molecular mapping of genes for crop resistance to the greenbug, Schizaphis graminum Rondani, will facilitate selection of greenbug resistance in breeding through marker-assisted selection and provide information for map-based gene cloning. In the present study, microsatellite marker and deletion line analyses were used to map greenbug resistance genes in five newly identified wheat germplasms derived from Aegilops tauschii. Our results indicate that the Gb genes in these germplasms are inherited as single dominant traits. Microsatellite markers Xwmc157 and Xgdm150 flank Gbx1 at 2.7 and 3.3 cM, respectively. Xwmc671 is proximately linked to Gba, Gbb, Gbc and Gbd at 34.3, 5.4, 13.7, 7.9 cM, respectively. Xbarc53 is linked distally to Gba and Gbb at 20.7 and 20.2 cM, respectively. Xgdm150 is distal to Gbc at 17.9 cM, and Xwmc157 is distal to Gbd at 1.9 cM. Gbx1, Gba, Gbb, Gbc, Gbd and the previously characterized Gbz are located in the distal 18% region of wheat chromosome 7DL. Gbd appears to be a new greenbug resistance gene different from Gbx1 or Gbz. Gbx1, Gbz Gba, Gbb, Gbc and Gbd are either allelic or linked to Gb3.     

A comparison of five distance‐based methods for spatial pattern analysis

Abstract. The behaviour of five statistics (extensions of Pielou's, Clark and Evansapos;, Pollard's, Johnson & Zimmer's, and Eberhardt's statistics, which are denoted as P_i, C_e, P_o, J_z and E_b respectively) that involve the distance from a random point to its jth nearest neighbour were examined against several alternative patterns (lattice‐based regular, inhomogeneous random, and Poisson cluster patterns) through Monte Carlo simulation to test their powers to detect patterns. The powers of all the five statistics increase as distance order j increases against inhomogeneous random pattern. They decrease for P_i and C_e and increase for P_o, J_z, and E_b against regular and Poisson cluster patterns. P_o, J_z, and E_b can reach high powers with the third or higher order distances in most cases. However, P_o is recommended because no extra information is needed, it can reach a high power with the second or third distance even though the sample size is not large in most cases, and the test can be performed with an approximate χ² distribution associated with it. When a regular pattern is expected, J_z is recommended because it is more sensitive to lattice‐based regular pattern than P_o and E_b, especially for the first distance. However, simulation tests should be used because the speed of convergence of J_z to normal distribution is very slow.     

Hemibranchiate sphaeromatids (Crustacea: Isopoda) from Queensland, Australia, with a world-wide review of the genera discussed

All known Queensland species of the isopod family Sphaeromatidae, subfamily Sphaeromatinae (= hemibranchs), are discussed. The following new taxa are erected: Calcipila cornuta, gen. nov., sp. nov. ; Cymodoce tribullis, sp. nov. ; Cymodoce bipapilla, sp. nov. ; Paracilicaea aspera, sp. nov. ; Cilicaeopsis glebosa, sp. nov. ; Cilicaeopsis furculata, sp. nov. ; Cilicaea calcarifera, sp. nov. ; Zuzara curtispina, sp. nov. ; Zuzara digitata, sp. nov. ; and Clianella brucei, sp. nov. Exosphaeroma intermedium Baker is transferred to the genus Sphaeroma Latreille. The genus Dynoides Barnard is reviewed and its current synonymy is contested. With several new records, this brings the total number of sphaeromatid species known from Queensland to 49, 24 of which are in the subfamily Sphaeromatinae. A checklist of all sphaeromatid species occurring in Queensland waters is given. From the rest of Australia: Cymodoce tuberculata Haswell is given the replacement name Cymodoce haswelli, nom. nov. ; Cymodoce granulata Miers is made a junior synonym of Cerceis trispinosa (Haswell) (subfamily Dynameninae); Zuzara diadema Leach, Z. dicantha (Milne Edwards) and Z. Integra Haswell are made junior synonyms of Z. semipunctata Leach; Cilicaeopsis dakini Tattersall is tentatively transferred to the genus Paracilicaea Stebbing. The genera discussed are reviewed world-wide and among the non-Australian species: Exosphaeroma papillae Bayliff is transferred to the genus Sphaeroma; Sphaeroma irakiensis Ahmed is made a junior synonym of Sphaeroma annandalei annandalei Stebbing; Cymodoce richardsoniae Nobili is shown to be distinct from Cymodoce truncata Leach; Cymodoce eupyga Nobili is transferred to the genus Paracilicaea; Dynoides amblysinus Pillai, Dynoides castroi Loyola e Silva and Exosphaeroma globicaudum (Dana) are transferred to the genus Clianella Boone; Dynoides brasiliensis (Loyola e Silva; and Sphaeroma savignn Milne Edwards sensu Dana, 1853 are declared to be conspecific with Clianella castroi. The name Sorrentosphaera Verhoeff is made a junior synonym of Dynamene Leach (subfamily Dynameninae.     

Specificity of Chroomonas (Cryptophyceae) as a source of kleptochloroplast for Nusuttodinium aeruginosum (Dinophyceae)

The unarmoured dinoflagellate Nusuttodinium aeruginosum retains a kleptochloroplast, which is a transient chloroplast stolen from members of the cryptomonad genus, Chroomonas. Both N. aeruginosum and the closely related N. acidotum have been shown to restrict their diet to a limited number of species of this blue‐green genus of cryptophyte. However, it is still unclear how flexible the predators are with regard to the ingestion and utilization of Chroomonas spp. as a source of kleptochloroplast. To address specificity of cryptomonad in N. aeruginosum, we collected the cells of N. aeruginosum from several ponds in Japan, and analysed the phylogeny of the kleptochloroplasts based on their plastidial 16S rDNA sequences. All sequences obtained in this study were restricted to only one (the subclade 4) of four subclades known to comprise the Chroomonas/Hemiselmis clade. Therefore, N. aeruginosum is specific in its dietary requirements, selecting their prey within the subclade level.