Mapping of the SLA complex of miniature swine: mapping of the SLA gene complex by pulsed field gel electrophoresis.

The overall order of the regions of the swine major histocompatibility complex (MHC), the SLA complex, was determined by pulsed field gel electrophoresis (PFGE). It was found that the order of the regions is class II-class III-class I. A class I probe hybridized to a 420 kb Mlu I and a 420 kb Not I fragment as did a class III probe for C2. None of the class II probes hybridized to these fragments. Thus, linkage of class I to class III was shown. The class III C2, Bf, and C4 genes were found to residue in a 190 kb Not I fragment. Linkage of class III and class II genes was shown when both the class III C4 and the class II DR probes hybridized to the same 195 kb Sac II and 340 kb Not I fragments. The class I probe did not hybridize to these fragments. The order of the regions, class II-class III-class I, is similar to that of human MHC genes and may have been conserved in evolution so that coordinated expression of MHC genes could be achieved.     

Variation and inheritance of the arachin polypeptides of groundnut (Arachis hypogaea L.)

Summary Variation in the arachin polypeptides of groundnut genotypes was observed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Three regions could be observed on the electropherogram. Region 1, corresponding to conarachin, did not show any variation; region 2, consisting of arachin acidic subunits, showed variation; region 3, containing the arachin basic subunits, did not show any variation. There are four varietal classes of arachin polypeptide patterns: class A comprised three acidic subunits of arachin of molecular weights 47.5, 45.1 and 42.6 kd and a basic subunit of 21.4 kd; class B, with three acidic subunits of molecular weights 47.5, 45.1 and 41.2 kd and a basic subunit of 21.4 kd; class C of an additive pattern of class A and class B; class D, of two acidic polypeptides of 47.5, 45.1 kd and the basic 21.4 kd subunit. Of the 90 genotypes studied, 73% belong to class A, 15% to class B and 6% each to class C and D. Analysis of F₂ seeds from a cross between class A and class B genotypes showed that the two polypeptides (42.6 kd and 41.2 kd) are coded by nonallelic genes and also revealed that class C and class D patterns arose as a result of hybridisation between class A and class B. A. monticola, the progenitor of A. hypogaea, showed a pattern similar to the additive pattern of class A and class B while some diploid Arachis species had the 41.2 kd polypeptide. Based on arachin polypeptide patterns the probable origin of A. hypogaea has been suggested.     

Revision of the carabid genus <Emphasis Type="Italic">Meroctenus</Emphasis> Gemminger et Harold,with a new status of <Emphasis Type="Italic">Xenodochus</Emphasis> Andrewes (Coleoptera,Carabidae: Harpalini)

Originally described as a monotypical genus with unclear taxonomic position from Sudan, Meroctenus Gemminger et Harold, 1868 is treated as a polytypical genus of the Selenophori genus group with two subgenera: Meroctenus s. str. and Xenodochus Andrewes, 1941, stat. n. (the latter was previously considered a distinct genus). Within Meroctenus, two species are recognized: M. (Meroctenus) crenulatus Chaudoir, 1843 (type species) and M. (M.) mediocris (Andrewes, 1936), comb, n., transferred to Meroctenus s. str. from Xenodochus. A new subspecies M. (M.) crenulatus orientalis subsp. n. is described from Pakistan. Diagnoses of the genus Meroctenus in new interpretation as well as of its two subgenera are discussed, and a taxonomic review of the subgenus Meroctenus s. str. with a key to the species and subspecies is provided. The following synonymy is proposed: Meroctenus Gemminger et Harold, 1868 = Paregaploa Müller, 1947, syn. n.; Meroctenus crenulatus (Chaudoir, 1843) = Egaploa (Paregaploa) conviva Müller, 1947, syn. n. Lectotypes are designated for Ctenomerus crenulatus Chaudoir, 1843 and Xenodus mediocris Andrewes, 1936.     

Revision of <Emphasis Type="Italic">Podocotyloides</Emphasis> Yamaguti, 1934 (Digenea: Opecoelidae), resurrection of <Emphasis Type="Italic">Pedunculacetabulum</Emphasis> Yamaguti, 1934 and the naming of a cryptic opecoelid species

Despite morphological and ecological inconsistencies among species, all plagioporine opecoelids with a pedunculate ventral sucker are currently considered to belong in the genus Podocotyloides Yamaguti, 1934. We revise the genus based on combined morphological and phylogenetic analyses of novel material collected from haemulid fishes in Queensland waters that we interpret to represent species congeneric with the type-species, Pod. petalophallus Yamaguti, 1934, also known from a haemulid, off Japan. Our phylogenetic analysis demonstrates polyphyly of Podocotyloides; prompts us to resurrect Pedunculacetabulum Yamaguti, 1934; and suggests that Pod. brevis Andres & Overstreet, 2013, from a deep-sea congrid in the Caribbean, and Pod. parupenei (Manter, 1963) Pritchard, 1966 and Pod. stenometra Pritchard, 1966, from mullids and chaetodontids, respectively, on the Great Barrier Reef, may each represent a distinct genus awaiting recognition. Our revised concept of Podocotyloides requires a pedunculate ventral sucker, but also a uterine sphincter prior to the genital atrium, a petalloid cirrus appendage, restriction of the vitelline follicles to the hindbody, and for the excretory vesicle to reach to the level of the ventral sucker. Of about 20 nominal species, we recognise just three in Podocotyloides (sensu stricto): Pod. petalophallus, Pod. gracilis (Yamaguti, 1952) Pritchard, 1966 and Pod. magnatestes Aleshkina & Gaevskaya, 1985. We provide new records for Pod. gracilis, and propose two new species of Podocotyloides, Pod. australis n. sp. and Pod. brevivesiculatus n. sp., and one new Pedunculacetabulum species, Ped. inopinipugnus n. sp., all from haemulids. Podocotyloides australis is morphologically indistinguishable from Pod. gracilis, and exploits the same definitive host, but is genetically and biogeographically distinct. It is thus a cryptic species, the first such opecoelid to be formally named.     

Initial establishment of vegetation in a man-made coastal area in Denmark

A man-made coastal area (8 km long, 300 m wide), constructed from seed-free, marine sand was investigated from 1978 to 1983 as regards relief, soil properties, and establishment of vegetation.
The following developments were apparent:

• 1. 

  The outer shore zone changed from a Cakile -dominated vegetation to a sparse and less diverse vegetation.
• 2. 

  The inner shore zone maintained spontaneous Ammophila as dominant and developed into a mobile dune with changing species.
• 3. 

  The outer dune slope with planted Ammophila developed into a mobile dune dominated by vigorous Ammophila.
• 4. 

  The dune zone with planted Ammophila: The outer part developed towards a somewhat fixed dune with increasing diversity. The inner part developed into a diverse and more fixed dune community with mainly Festuca rubra.
• 5. 

  The inner dune slope developed into a vegetation comprising few species.
• 1. 

  The grassland zone, initially sown with Festuca rubra and Lolium perenne , changed into a grass-herb-vegetation dominated by Festuca rubra , with a slowly increasing number of immigrating species, changing from annuals to perennials, in particular species of Fabaceae and Hippophaë.

     

Induction of linked suppression in addition to the donor H-2 class I-specific unresponsiveness in recipient T cells by transfusing class I plus class II-disparate, but not class I alone-disparate, bone marrow cells

This study was undertaken to determine whether bone marrow (BM) cells contain a cell population with the capacity to induce an unresponsiveness of T cells specific to the BM self-H-2 class I antigens in vivo, i.e., veto cell population. Recombinant or congenic mice were infused intravenously with H-2-incompatible BM cells. One to several weeks later, donor H-2-and irrelevant H-2-specific responses in mixed lymphocyte reaction cultures of recipient T cells were assessed. Transfusion of H-2-incompatible BM of C57BL/10 (B10) recombinant strains caused a long-lasting cytotoxic T lymphocyte (CTL) unresponsiveness to the donor class I antigens in recipient lymph node cells. When class I plus class II-disparate BM cells were transfused, an anti-donor class I CTL response and a response against a third-party class I antigen, which was presented on the stimulator cells coexpressing the donor class I and class II, were significantly suppressed. This linked suppression lasted for less than 2 weeks after transfusion. Transfusion of class I-alone-disparate BM induced the donor class I-specific CTL unresponsiveness, but not the linked suppression. The induction of linked suppression was prevented considerably by transfusing nylon wool-nonadherent BM or by treating recipients with cyclophosphamide 2 days before transfusion. An anti-third-party class I CTL response, stimulated in vitro with fully allogeneic spleen cells, was not hampered by the BM transfusion. Coculturing the lymph node (LN) cells obtained from the class I plus class II-disparate BM recipient with normal LN cells interfered with the generation of both anti-donor class I and anti-linked third-party class I CTL, whereas, coculturing LN cells from the class I alone-disparate BM recipient inhibited neither specificity of CTL generation. Transfusion of class I plus class II-disparate BM resulted in a significant suppression of the donor class II-specific proliferative response. In contrast, transfusion of class I alone-disparate BM did not suppress any proliferative responses, including even a "linked" third-party class II-specific response. Transfusion of bm 1, (B6 X bm 1)F1, or (bm 1 X bm 12)F1 BM to B6 did not induce unresponsiveness in bm 1-specific CTL responses. However, the transfusion resulted in a significant suppression of bm 1-reactive proliferative response of recipient LN cells.(ABSTRACT TRUNCATED AT 400 WORDS)     

Functional expression of a heterologous major histocompatibility complex class I gene in transgenic mice.

The regulated expression of major histocompatibility complex class I antigens is essential for assuring proper cellular immune responses. To study H-2 class I gene regulation, we have transferred a foreign class I gene to inbred mice and have previously shown that the heterologous class I gene was expressed in a tissue-dependent manner. In this report, we demonstrate that these mice expressed the transgenic class I molecule on the cell surface without any alteration in the level of endogenous H-2 class I antigens. Skin grafts from transgenic mice were rapidly rejected by mice of the background strain, indicating that the transgenic antigen was expressed in an immunologically functional form. As with endogenous H-2 class I genes, the class I transgene was inducible by interferon treatment and suppressible by human adenovirus 12 transformation. Linkage analysis indicated that the transgene was not closely linked to endogenous class I loci, suggesting that trans-regulation of class I genes can occur for class I genes located outside the major histocompatibility complex.     

Expression of invariant chain can cause an allele-dependent increase in the surface expression of MHC class I molecules

Invariant chain (Ii) has been shown to play a significant part in the assembly of MHC class II molecules. Ii also binds to MHC class I, although it is not known when this first occurs or whether it can affect class I assembly. Our examination of lysates of L(d)-transfected T2 cells showed that Ii bound intracellularly to folded, but not to open, forms of MHC class I. Furthermore, addition of peptides to the lysates dissociated Ii from the Ii-folded MHC class I complex. Thus, unlike other known chaperones, Ii associates only with folded, peptide-free class I molecules. To determine whether Ii can affect MHC class I transport and surface expression, we used both wild-type Ii and a mutant Ii that lacked the endosomal targeting sequence. Neither Ii nor Ii(Delta 20) increased the rate of MHC class I migration; however, Ii and (to a greater extent) Ii(Delta 20) increased cell surface expression of MHC class I. In HeLa cells, this effect was allele-specific, affecting HLA-A28 more than -B75. Ii also increased the surface expression of K(b) more than D(b) on Panc02 pancreatic adenocarcinoma cells. Neither form of Ii was detectable at the cell surface with MHC class I, indicating that Ii had exercised its effect on class I intracellularly. In total, these data suggest that Ii can bind peptide-free folded class I/beta(2)m heterodimers, but not open MHC class I heavy chains, in the endoplasmic reticulum, and that Ii can facilitate the surface expression of the MHC class I molecule.     

The mathematical model of concentration polarization coefficient in membrane transport and volume flows

In this paper, the authors investigate the membrane transport of aqueous non-electrolyte solutions in a single-membrane system with the membrane mounted horizontally. The purpose of the research is to analyze the influence of volume flows on the process of forming concentration boundary layers (CBLs). A mathematical model is provided to calculate dependences of a concentration polarization coefficient (ζ _s ) on a volume flux (J _vm ), an osmotic force (Δπ) and a hydrostatic force (ΔP) of different values. Property ζ _s ?=?f(J _vm ) for J _vm ?>?0 and for J _vm ?≈?0 and property ζ _s ?=?f(ΔC ₁) are calculated. Moreover, results of a simultaneous influence of ΔP and Δπ on a value of coefficient ζ _s when J _vm ?=?0 and J _vm ?≠?0 are investigated and a graphical representation of the dependences obtained in the research is provided. Also, mathematical relationships between the coefficient ζ _s and a concentration Rayleigh number (R _C ) were studied providing a relevant graphical representation. In an experimental test, aqueous solutions of glucose and ethanol were used.     

Efficient incorporation of HLA class II onto human immunodeficiency virus type 1 requires envelope glycoprotein packaging

HLA class II DR is one of the most abundant cell surface proteins incorporated onto human immunodeficiency virus type 1 (HIV-1) during budding. The mechanism for HLA class II protein incorporation is not known and may involve a viral protein. To determine whether Env affects HLA class II protein incorporation, HIV-1 virions, either with or without Env on their surface, were produced from HLA class II-expressing cells and analyzed by whole-virus immunoprecipitation with antisera against HLA class II proteins. HLA class II proteins were detected on virions only when wild-type Env was incorporated, while similar experiments showed that HLA class I proteins were incorporated independent of Env packaging. Therefore, the packaging of HIV-1 Env protein is required for the efficient incorporation of HLA class II but not class I proteins into the virion. Analysis of two Env mutants revealed that the presence of a 43-amino-acid sequence between amino acids 708 and 750 in the gp41(TM) cytoplasmic tail was required for efficient incorporation of HLA class II proteins. These data show that HIV-1 actively incorporates HLA class II proteins in a process that, either directly or indirectly, requires Env.     

Effect of decreasing the affinity of the class II-associated invariant chain peptide on the MHC class II peptide repertoire in the presence or absence of H-2M

The class II-associated invariant chain peptide (CLIP) region of the invariant chain (Ii) directly influences MHC class II presentation by occupying the MHC class II peptide-binding groove, thereby preventing premature loading of peptides. Different MHC class II alleles exhibit distinct affinities for CLIP, and a low affinity interaction has been associated with decreased dependence upon H-2M and increased susceptibility to rheumatoid arthritis, suggesting that decreased CLIP affinity alters the MHC class II-bound peptide repertoire, thereby promoting autoimmunity. To examine the role of CLIP affinity in determining the MHC class II peptide repertoire, we generated transgenic mice expressing either wild-type human Ii or human Ii containing a CLIP region of low affinity for MHC class II. Our data indicate that although degradation intermediates of Ii containing a CLIP region with decreased affinity for MHC class II do not remain associated with I-A(b), this does not substantially alter the peptide repertoire bound by MHC class II or increase autoimmune susceptibility in the mice. This implies that the affinity of the CLIP:MHC class II interaction is not a strong contributory factor in determining the probability of developing autoimmunity. In contrast, in the absence of H-2M, MHC class II peptide repertoire diversity is enhanced by decreasing the affinity of CLIP for MHC class II, although MHC class II cell surface expression is reduced. Thus, we show clearly, in vivo, the critical chaperone function of H-2M, which preserves MHC class II molecules for high affinity peptide binding upon dissociation of Ii degradation intermediates.     

Mutations in <Emphasis Type="Italic">CsPID</Emphasis> encoding a Ser/Thr protein kinase are responsible for round leaf shape in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Key message

Two round-leaf mutants, rl-1 and rl-2, were identified from EMS-induced mutagenesis. High throughput sequencing and map-based cloning suggested CsPID encoding a Ser/Thr protein kinase as the most possible candidate for rl-1. Rl-2 was allelic to Rl-1.

Abstract

Leaf shape is an important plant architecture trait that is affected by plant hormones, especially auxin. In Arabidopsis, PINOID (PID), a regulator for the auxin polar transporter PIN (PIN-FORMED) affects leaf shape formation, but this function of PID in crop plants has not been well studied. From an EMS mutagenesis population, we identified two round-leaf (rl) mutants, C356 and C949. Segregation analysis suggested that both mutations were controlled by single recessive genes, rl-1 and rl-2, respectively. With map-based cloning, we show that CsPID as the candidate gene of rl-1; a non-synonymous SNP in the second exon of CsPID resulted in an amino acid substitution and the round leaf phenotype. As compared in the wild type plant, CsPID had significantly lower expression in the root, leaf and female flowers in C356, which may result in the less developed roots, round leaves and abnormal female flowers, respectively in the rl-1 mutant. Among the three copies of PID genes, CsPID, CsPID2 and CSPID2L (CsPID2-like) in the cucumber genome, CsPID was the only one with significantly differential expression in adult leaves between WT and C356 suggesting CsPID plays a main role in leaf shape formation. The rl-2 mutation in C949 was also cloned, which was due to another SNP in a nearby location of rl-1 in the same CsPID gene. The two round leaf mutants and the work presented herein provide a good foundation for understanding the molecular mechanisms of CsPID in cucumber leaf development.

     

Population biology of parasites of striped mullet, Mugil cephalus L. I. Monogenea

Young-of-the-year (class 0) and yearling (class 1) striped mullet, Mugil cephalus , were collected from Sapelo Island, Georgia from May 1970 to June 1971 to study the development, seasonal abundance and relationship of environmental variables to parasitic populations. The number of species of parasites increased with age of the host. Initial infection appeared to be influenced by closeness of association of mullet age classes, by the period of abundance of a parasite on class I mullet and by the mobility of the infective parasitic stage. Fluctuations in intensity and prevalence of a parasite on class 0 mullet were similar to those of class I mullet after the initial infection. Ancyrocephalus vanbenedenii was first observed on class 0 mullet in March. Intensity was high on both classes in spring and on reproductively active mullet in late autumn. Prevalence on both classes was above 80% except in late summer. Polyclithrum mugilis was not observed on class 0 mullet until August even though intensity and prevalence on class I mullet was highest during early spring. Gyrodactylus mugelus did not occur on class 0 mullet but appeared on class I mullet during late summer. Microcotyle psuedomugilis was observed on class 0 mullet in early summer and Metamicrocolyla maeracantha in October. Both species occurred but at a low intensity on class I mullet.     

Mining statistically-solid <Emphasis Type="Italic">k</Emphasis>-mers for accurate NGS error correction

Background

NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-mer most likely contains errors. An intensively investigated problem is to find a good frequency cutoff f₀ to balance the numbers of solid and weak k-mers. Once the cutoff is determined, a more challenging but less-studied problem is to: (i) remove a small subset of solid k-mers that are likely to contain errors, and (ii) add a small subset of weak k-mers, that are likely to contain no errors, into the remaining set of solid k-mers. Identification of these two subsets of k-mers can improve the correction performance.

Results

We propose to use a Gamma distribution to model the frequencies of erroneous k-mers and a mixture of Gaussian distributions to model correct k-mers, and combine them to determine f₀. To identify the two special subsets of k-mers, we use the z-score of k-mers which measures the number of standard deviations a k-mer’s frequency is from the mean. Then these statistically-solid k-mers are used to construct a Bloom filter for error correction. Our method is markedly superior to the state-of-art methods, tested on both real and synthetic NGS data sets.

Conclusion

The z-score is adequate to distinguish solid k-mers from weak k-mers, particularly useful for pinpointing out solid k-mers having very low frequency. Applying z-score on k-mer can markedly improve the error correction accuracy.

     

Unusual stilbenoids and a stilbenolignan from seeds of Syagrus romanzoffiana

Stilbenoids, syagrusins A-B (1-2), and a stilbenolignan, 5-hydroxyaiphanol (3), along with three known phenylpropanoids (4-6), were isolated from seeds of Syagrus romanzoffiana. Compounds 1 and 2 possess unusual 1,4,4a,9a-tetrahydrofluoren-9-one and bicyclo[3.3.0]octanedione skeletons, respectively, whereas compound 3 is a stilbenolignan belonging to a very rare structural class of plant secondary metabolites. Their structures were elucidated by spectroscopic analyses. Compounds 1-3 exhibited moderate inhibitory activity against α-glucosidase with IC₅₀ values of 16.9 μM (1), 23.7 μM (2) and 12.8 μM (3), respectively.     

Molecular analyses of <Emphasis Type="Italic">Ficus erecta</Emphasis> and its allies within the subsection <Emphasis Type="Italic">Frutescentiae</Emphasis> (Moraceae)

Ficus (Moraceae) is a keystone group in tropical and subtropical forests with remarkable diversity of species and taxonomical challenges as a consequence of fig–pollinator coevolution. Ficus subsect. Frutescentiae includes about 30 species that are predominantly shrubs or small trees with Terminalia branching. Many of these species are difficult to delimit morphologically, and the group includes a tangle of uncertain taxa and incorrectly applied names. We conducted a phylogenetic analysis with internal and external transcribed spacer data (ITS and ETS) and data from 18 polymorphic microsatellite loci to evaluate the species status of the most perplexing members of this subsection. The results confirm the monophyly of subsect. Frutescentiae, with F. pedunculosa as sister to the rest. The F. erecta complex comprises approximately 17 taxa: F. erecta, F. abelii, F. boninsimae, F. nishimurae, F. iidaiana, F. gasparriniana var. laceratifolia, F. gasparriniana var. viridescens, F. pyriformis, F. stenophylla, F. fusuiensis, F. fengkaiensis, F. sinociliata, F. tannoensis, F. vaccinioides, F. formosana, F. pandurata, and F. periptera. The last five of these were supported as good species, while the others were not well supported by the present evidence. Evidence also supported the status of the non-F. erecta complex species including. F. pedunculosa, F. ischnopoda, F. heteromorpha, and F. variolosa. Ficus filicauda and F. neriifolia are possibly conspecific. The species status of F. potingensis should be restored and it should be treated as a member of section Eriosycea. Identification of the remaining taxa (F. gasparriniana var. esquirolii, F. ruyuanensis, F. daimingshanensis, F. chapaensis, F. changii, F. trivia, and F. tuphapensis) and their relationships to the F. erecta complex were not clarified. As a whole, only ten species in this subsection are confirmed, one is excluded, one is synonymous, and the others are either unresolved or short of samples. There appears to be a consistent genetic background among these unresolved groups, which suggests that repeated hybridization (as a result of pollinator host shifts) has filled up the interspecific gaps during the fig–pollinator coevolution process.     

Mapping of the SLA complex of miniature swine: Mapping of the SLA gene complex by pulsed field gel electrophoresis

The overall order of the regions of the swine major histocompatibility complex (MHC), the SLA complex, was determined by pulsed field gel electrophoresis (PFGE). It was found that the order of the regions is class II-class III-class I. A class I probe hybridized to a 420 kbMlu I and a 420 kbNot I fragment as did a class III probe forC2. None of the class II probes hybridized to these fragments. Thus, linkage of class I to class III was shown. The class IIiC2, Bf, andC4 genes were found to reside in a 190 kbNot I fragment. Linkage of class III and class II genes was shown when both the class IIiC4 and the class IiDR probes hybridized to the same 195 kbSac II and 340 kbNot I fragments. The class I probe did not hybridize to these fragments. The order of the regions, class II-class III-class I, is similar to that of human MHC genes and may have been conserved in evolution so that coordinated expression of MHC genes could be achieved.