Occurrence of met-enkephalin,met-enkephalin-Arg6-Phe7 and met-enkephalin-Arg6-Gly7-Leu8 in gastrin cells of hog antral mucosa

Summary Region-specific antisera to three enkephalins: met-enkephalin, met-enkephalin-Arg⁶-Phe⁷ and met-enkephalin-Arg⁶-Gly⁷-Leu⁸, together with four region specific antisera to progastrin: C-terminal G17 specific, N-terminal G34 specific, cryptic peptides A- and B-specific, were used in immunohistochemical studies of hog antral mucosa. A sub-population (6–10%) of the gastrin-containing endocrine cells (G-cells) was found to react with antisera to met-enkephalin, met-enkephalin-Arg⁶-Phe⁷ and met-enkephalin-Arg⁶-Gly⁷-Leu⁸. About 30% of all the enkephalin-containing cells were identified as G-cells. The results indicate that a fraction of G-cells produces both enkephalin-like peptides and gastrin.     

Serological and biological variations of African cassava mosaic virus, in Nigeria

To determine the occurrence of variants of African cassava mosaic virus, 316 cassava leaf samples were collected from mosaic‐affected cassava plants in 254 farmers. fields in 1997 and 1998, covering the humid forest, coastal/derived, southern Guinea and northern Guinea savannas and arid and semi‐arid agroecologies of Nigeria. The samples were tested in triple antibody sandwich enzyme‐linked immunosorbent assay using a panel of 10 monoclonal antibodies (MAbs) against the virus in which 29 reaction patterns were observed. In cluster analysis, nine serotypes were obtained at 0.80 Jaccard similarity coefficient index in which at least 50% of isolates of each serotype reacted alike. The serotypes ranged between two extremes: serotype 1 with 90% isolates reacting with the 10 MAbs and serotype 8 in which 90% of its isolates failed to react with the antibodies. Isolates of serotypes 1, 2, 4 and 8 were widely distributed while those of the other serotypes were estricted to certain agroecologies. Four representative isolates 227 (serotype 1), 231 (serotype 2), 235 and 283 (serotype 8) elicited different responses in Nicotiana, benthamiana, with isolate 283 not able to infect this and other test plants used. The serological variations did not necessarily reflect the biological variations. In polymerase chain reaction tests, one out of the five pairs of ACMV primers tested distinguished only isolate 283. The humid forest, derived/coastal and southern Guinea savannas where most of the crop is grown in Nigeria had a high number of variants, which makes the agroecologies suitable for the selection of resistant cassava clones against ACMV.     

A partially deficient and atypical equine transferrin variant, TF N

A new, partially deficient and phenotypically atypical transferrin variant, TF N, was detected in sera of a number of Finnhorses belonging to one family. The variant was inherited codominantly. In polyacrylamide gel electrophoresis (pH9.0) of sera, variant N appeared as a single weak band migrating slightly faster than the main anodal band of variant M. After immunoblotting or isolation an additional, still weaker, faster band was observed as well as some trace bands. The cathodal component, which is present in other transferrin variants, could not be convincingly proved. The main component of variant N contained four sialic acid residues.     

Characterization of two new electrophoretic variants of human triosephosphate isomerase: Stability,kinetic, and immunological properties

Two new electrophoretic variants of human triosephosphate isomerase (TPI) have been partially purified and characterized. The TPI Manchester variant, a cathodally migrating electrophoretic allozyme identified in an individual with the phenotype TPI 1-Manchester, is associated with a normal level of enzyme activity in erythrocytes and normal kinetic properties. It is very thermolabile at 55 and 57° C, although it is not uniquely sensitive to either guanidine-HCl or urea denaturation. The TPI Hiroshima-2 variant is an anodally migrating allozyme (the phenotype of proband is TPI 1-Hiroshima-2) with normal activity and kinetic properties and also normal stability characteristics. It is inactivated less by antisera raised against normal human TPI than either the normal or the Manchester allozyme. Dissociation-reassociation experiments utilizing these allozymes have confirmed that normal human red blood cell TPI isozymes are produced by a sequence of reactions (presumably deamidations) involving alternating subunits.Financial support was derived from Contract EY-77-C-02-2828 from the Department of Energy.     

Analysis of genetic variation affecting the relative activities of fast and slow ADH dimers in Drosophila melanogaster heterozygotes

When Adh ^F /Adh ^S heterozygote homogenates are stained after electrophoresis, considerable variation is observed in the activity ratio of the FF dimer to the SS dimer. Two Adh ^S strains showed a sharp, consistent difference when crossed to a common Adh ^F strain. Optical scanning and genetic analysis confirmed that this difference originates close to the Adh locus. Since the morphs varied concordantly in their activities on numerous alcohols, and since aging and heat-treatment experiments failed to reveal a stability difference, it is proposed that the difference is regulatory in nature, affecting ADH synthesis and primarily cis-acting. A survey of wild flies revealed additional variation in the FF/SS activity ratio. Further genetic analysis showed that the basis of this variation is not restricted to the second chromosome. Furthermore, modification of the activity ratio implies some degree of allelespecificity on the part of the modifiers.This work was supported in part by money collected by Jewish Community of Iowa City, Iowa, and by NSF Grant 76-01903 to Roger Milkman.     

PTGS1, PTGS2, ALOX5, ALOX12, ALOX15, and FLAP SNPs: interaction with fatty acids in colon cancer and rectal cancer

Dietary polyunsaturated fatty acids (PUFAs) can be converted to prostaglandins and leukotrienes. Oxygenation of omega-6 PUFAs generally results in the production of pro-inflammatory mediators, whereas oxygenated products of omega-3 (n-3) PUFAs generally have lower inflammatory activity. We hypothesize that elevated n-3 PUFA intakes from fish are associated with lower risk of colorectal cancer among those with genetic variants that result in higher levels of pro-inflammatory mediators. In population-based case–control studies of colon (case n = 1,574) and rectal cancer (case n = 791) and disease-free controls (n = 2,969), we investigated interactions between dietary fatty acid intake and 107 candidate polymorphisms and tagSNPs in PTGS1, PTGS2, ALOX12, ALOX5, ALOX15, and FLAP. The two studies used an identical genotyping protocol. We observed interactions and statistically significant increases in colon cancer risk for low docosahexaenoic acid intake among those with the PTGS1 rs10306110 (−1,053 A > G) variant genotypes (OR = 1.6, 95 % confidence interval = 1.1–2.3, adj. p = 0.06) and rectal cancer risk for low total fat intake among those with the variant PTGS1 rs10306122 (7,135 A > G) (OR_vs.wt = 1.80, 1.02–2.99; adj. p = 0.08). The ALOX15 rs11568131 (10,339 C > T) wild type in combination with a high inflammation score (low EPA intake, high AA intake, no regular NSAID use, high BMI, smoking) was associated with increased colon cancer risk (OR = 2.28, 1.7–3.07). Rectal cancer risk was inversely associated with a low inflammation score among PTGS2 rs4648276 (3,934 T > C) variant allele carriers (OR = 0.49, 0.25–0.75). Overall, these data provide some modest evidence for interactions between dietary fat intake and genetic variation in genes involved in eicosanoid metabolism and colorectal cancer risk.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-012-0302-x) contains supplementary material, which is available to authorized users.     

Protein structure-based evaluation of missense variants: Resources,challenges and future directions

We provide an overview of the methods that can be used for protein structure-based evaluation of missense variants. The algorithms can be broadly divided into those that calculate the difference in free energy (ΔΔG) between the wild type and variant structures and those that use structural features to predict the damaging effect of a variant without providing a ΔΔG. A wide range of machine learning approaches have been employed to develop those algorithms. We also discuss challenges and opportunities for variant interpretation in view of the recent breakthrough in three-dimensional structural modelling using deep learning.     

Bovine serum transferrin phenotypes AA,D1D1, D2D2, EE: Their carbohydrate compositions and electrophoretic multiplicity

Samples of homozygous bovine serum transferrins have been prepared and their purity has been ascertained by immunological techniques and electrophoretic analysis in SDS. Measurements of carbohydrate composition show that no significant differences exist among the phenotypic variants AA, D₁D₁, D₂D₂, and EE. Chromatography of transferrin AA on DEAE-cellulose separated four subfractions, each of which corresponded well with one band obtained by polyacrylamide gel electrophoresis. Carbohydrate analyses of the individual subfractions did not show significant differences in sialic acid, hexose, or hexosamine contents. After desialylation with neuraminidase, each subfraction was converted to a major band and a minor band on gel electrophoresis. From the relative band positions of the desialylated transferrins, it was concluded that possession of sialyl residues by bovine transferrin is not the primary cause of electrophoretic multiplicity. Rather, sialic acid masks an underlying heterogeneity which most likely resides within the polypeptide chain. Further characterization of this heterogeneity will best be undertaken with the isolated asialotransferrin subfractions.This research was supported by Grants MT-4074 and MA-5554 from the Medical Research Council of Canada and a Senior Fellowship (to M. W. C. H.) from the Ontario Heart Foundation.     

Identification of Mob2, a Novel Regulator of Larval Neuromuscular Junction Morphology,in Natural Populations of Drosophila melanogaster

Although evolutionary changes must take place in neural connectivity and synaptic architecture as nervous systems become more complex, we lack understanding of the general principles and specific mechanisms by which these changes occur. Previously, we found that morphology of the larval neuromuscular junction (NMJ) varies extensively among different species of Drosophila but is relatively conserved within a species. To identify specific genes as candidates that might underlie phenotypic differences in NMJ morphology among Drosophila species, we performed a genetic analysis on one of two phenotypic variants we found among 20 natural isolates of Drosophila melanogaster. We discovered genetic polymorphisms for both positive and negative regulators of NMJ growth segregating within the variant line. Focusing on one subline, that displayed NMJ overgrowth, we mapped the phenotype to Mob2 [Monopolar spindle (Mps) one binding protein 2)], a gene encoding a Nuclear Dbf2 (Dumbbell formation 2)-Related (NDR) kinase activator. We confirmed this identification by transformation rescue experiments and showed that presynaptic expression of Mob2 is necessary and sufficient to regulate NMJ growth. Mob2 interacts in a dominant, dose-dependent manner with tricornered but not with warts, to cause NMJ overgrowth, suggesting that Mob2 specifically functions in combination with the former NDR kinase to regulate NMJ development. These results demonstrate the feasibility and utility of identifying genetic variants affecting NMJ morphology in natural populations of Drosophila. These variants can lead to discovery of new genes and molecular mechanisms that regulate NMJ development while also providing new information that can advance our understanding of mechanisms that underlie nervous system evolution.     

Modulation of mammalian cell growth by a choline analog,N-isopropylethanolamine

Summary The choline analog,N-isopropylethanolamine (IPE), inhibits the growth of both Chinese hamster ovary CHO-K₁ and mouse L-M cells by two kinetically distinct mechanisms; I, a reversible and concentration-dependent reduction in the logarithmic population doubling rate and the saturation density of cultures by low IPE levels in the media; and II, an irreversible and time-dependent killing of cells by high IPE concentrations. Both types of inhibition are independent of media depletion, cell density, or the time of treatment after cell plating; however, the actual IPE concentration that is necessary to elicit Type I or Type II inhibition in each cell line is dependent on the choline level of the media. Ethanolamine, methionine, or betaine have no effect on IPE-induced growth inhibition. From a mutagenized population of CHO-K₁ cells we isolated variant cell strains that are resistant to the lethal effect of IPE. It was determined that with both the wild type and variant strains the sensitivity of cells to growth inhibition by IPE (both Type I and Type II) was proportional to the degree by which choline uptake was inhibited by the analog. Retinoic acid, which inhibits the growth of some fibroblast and epithelial cell lines by a concentration-dependent reduction in population doubling rate and saturation density, behaves synergistically with IPE to inhibit the growth of CHO-K₁ cells. Dibutyryl cyclic AMP, on the other hand, causes only an additive increase in the growth inhibition of CHO-K₁ populations that also are treated with IPE. This article is based on work supported by contract DE-AC05-760R00033 from the U.S. Department of Energy to Oak Ridge Associated Universities.     

Novel Muscle-Specific Genes TCAP,TNNI1, and FHL1 in Cattle: SNVs,Linkage Disequilibrium,Combined Genotypes,Association Analysis of Growth Performance,and Carcass Quality Traits and Expression Studies

TCAP, TNNI1, and FHL1 regulate muscle growth and development. In this study, four single nucleotide variants (SNVs) were discovered in almost all of the exon and intron regions of the TCAP, TNNI1, and FHL1 genes using DNA pooled sequencing, polymerase chain reaction (PCR)-RFLP, and forced-PCR-RFLP methods in 576 cattle. Four SNVs were significantly associated with the growth performance and carcass quality traits of the cattle. In addition, the haplotype, haplotype frequency, and linkage disequilibrium coefficient of three sequence variants were also evaluated in the cattle population. Haplotype analysis demonstrated that eight haplotypes were present in the Qinchuan cattle population and no haplotypes were present in the Chinese Holstein population; haplotype 1 had the highest frequency in the Qinchuan (42.7%) population. Statistical analyses of 12 combined genotypes indicated that some were significantly associated with the growth performance and carcass quality traits of the Qinchuan cattle population. Moreover, the quantitative real-time polymerase chain reaction results demonstrated that the bovine TCAP, TNNI1, and FHL1 genes were exclusively expressed in muscle tissue. These data support the high potentials of the TCAP, TNNI1, and FHL1 as marker genes to improve the growth performance and carcass quality traits of Qinchuan cattle or other animals selection programs.     

广饶新石器时代人类头骨的小变异

通过对山东广饶新石器时代大汶口文化墓地90年代发掘的61具成年头骨进行小变异特征出现率的观察与统计并在此基础上进行聚类分析和主成分分析研究认为,广饶人群的蒙古人种地区类型属于东亚类型。同时本文结果提示,在明确蒙古人种地区类型的主成分分析研究中,贡献率较大的三个小变异特征为下颌舌骨肌线桥、舌下神经管二分、眶上孔,这将为以后人们用小变异方法从事这方面的研究中如何选择观察项目方面提供了基础。     

Morphometric characterisation of the native Honeybee,Apis mellifera Linnaeus, 1758, of Saudi Arabia

The rediscovery of the Minor Snake-eyed Skink, Ablepharus grayanus, from two different localities in Sistan and Baluchestan and Kerman Provinces, southeastern Iran is reported. A total of 24 specimens was examined based on morphometrics, colour pattern and pholidotic characters. One-way analyses of variance (ANOVA) based on morphometric measurements revealed significant differences in terms of the snoutvent length (SVL) and fore- and hind limb distances (GA) between eastern and western populations of Ablepharus pannonicus. The most distinguishing characters of Ablepharus grayanus are morphological features, especially ear opening status and scales around the midbody (18-20 versus 20-22). Based on morphological grounds, Ablepharus grayanus is clearly distinguished from A. pannonicus occurring in the eastern and western regions of the Iranian Plateau.     

Two new sheep haemoglobins, one of which is replaced by haemoglobin C in anaemia

Two new haemoglobin variants, provisionally named Hb G and Hb H, were found during a survey of 295 Welsh Mountain cross-bred sheep. Both haemoglobins appear to be beta chain variants controlled by genes allelic to those for the common forms Hb A and Hb B. Studies on an anaemic Hb AH and an Hb AG type sheep showed that Hb G, like Hb A, is replaced by Hb C in anaemia whereas Hb H, like Hb B, is not replaced.     

Alternate Junctions and Microheterogeneity of Tlr1, a Developmentally Regulated DNA Rearrangement in Tetrahymena thermophila

ABSTRACT. A large number of developmentally regulated DNA rearrangements occur during the development of the macronucleus in Tetrahymena thermophila , Tlr1 is a deletion element which has large inverted repeats near the rearrangement junctions and deletes more than 13 kbp of internal DNA. Previous analysis of caryonidal lines revealed alternate left junctions for the Tlr1 rearrangement in B strain cells. We show here that C2 strain Tetrahymena also use alternate rearrangement junctions. We have mapped and sequenced two additional rearrangement variants and find that both the left and right can vary over a range of approximately 200 bp. We also demonstrate the presence of sequence microheterogeneity in the most commonly found Tlr1 rearrangement product.     

New insights from the last decade of research in psychiatric genetics: discoveries,challenges and clinical implications

Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.     

基因结构变异检测方法综述

在人类基因组中结构变异(SVs),拷贝数变化(CNVs),单核苷酸多态性(SNP)是非常普遍的,而且和人类健康与疾病密切相关,因此检测这些结构变异对于人类生命健康非常重要。基于第二代基因测序平台,目前已经有很多结构变异检测算法,这些算法主要分为五大类:微阵列方法、读对方法、读深方法、分裂读取方法、序列组装方法。本文系统地阐述了这五类方法的基本原理、优缺点以及使用范围,并简要介绍了每一种方法的经典检测算法及应用范围、检测性能等,并对未来检测算法的研究提出了展望。