Escherichia coli malic enzymes: two isoforms with substantial differences in kinetic properties, metabolic regulation, and structure

Malic enzymes (MEs) catalyze the oxidative decarboxylation of malate in the presence of a divalent metal ion. In eukaryotes, well-conserved cytoplasmic, mitochondrial, and plastidic MEs have been characterized. On the other hand, distinct groups can be detected among prokaryotic MEs, which are more diverse in structure and less well characterized than their eukaryotic counterparts. In Escherichia coli, two genes with a high degree of homology to ME can be detected: sfcA and maeB. MaeB possesses a multimodular structure: the N-terminal extension shows homology to ME, while the C-terminal extension shows homology to phosphotransacetylases (PTAs). In the present work, a detailed characterization of the products of E. coli sfcA and maeB was performed. The results indicate that the two MEs exhibit relevant kinetic, regulatory, and structural differences. SfcA is a NAD(P) ME, while MaeB is a NADP-specific ME highly regulated by key metabolites. Characterization of truncated versions of MaeB indicated that the PTA domain is not essential for the ME reaction. Nevertheless, truncated MaeB without the PTA domain loses most of its metabolic ME modulation and its native oligomeric state. Thus, the association of the two structural domains in MaeB seems to facilitate metabolic control of the enzyme. Although the PTA domain in MaeB is highly similar to the domains of proteins with PTA activity, MaeB and its PTA domain do not exhibit PTA activity. Determination of the distinct properties of recombinant products of sfcA and maeB performed in the present work will help to clarify the roles of MEs in prokaryotic metabolism.     

Topical organization of the cat inferior colliculus under conditions of the simulated sound source motion

Binaurally presented click trains with gradually changing ITDs were used to imitate the sound source motion. Focal EP-trains from the cat inferior colliculus, IC, were recorded, and changing amplitude of the successive EPs following successive clicks was taken for estimation of the motion effect (ME). It was shown that a) in 25% of cases the ME depends on the motion direction; b) the ME is better presented ipsilaterally in respect to the recording point, with equal dependence on motion velocity both on the left and on the right; c) the ME phenomenon is connected with prevalence of contralateral afferentation as compared to the ipsilateral one; d) the ME is connected with inhibitory phenomena such as binaural suppression of monaural afferentation; e) the ME of the best amplitude is most pronounced in the ventrolateral area of the IC central nucleus, its localisation being near to that of the great multipolar neurones, whereas slightly and moderately pronounced MEs are presented rather uniformly over the central nucleus like the "basic" neurones are; MEs of different pronouncement are supposed to depend differently on effectiveness of ipsi- and contralateral stimulation--in accordance with properties of multipolar and "basic" neurons.     

Human metastable epiallele candidates link to common disorders

Metastable epialleles (MEs) are mammalian genomic loci where epigenetic patterning occurs before gastrulation in a stochastic fashion leading to systematic interindividual variation within one species. Importantly, periconceptual nutritional influences may modulate the establishment of epigenetic changes, such as DNA methylation at MEs. Based on these characteristics, we exploited Infinium HumanMethylation450 BeadChip kits in a 2-tissue parallel screen on peripheral blood leukocyte and colonic mucosal DNA from 10 children without identifiable large intestinal disease. This approach led to the delineation of 1776 CpG sites meeting our criteria for MEs, which associated with 1013 genes. The list of ME candidates exhibited overlaps with recently identified human genes (including CYP2E1 and MGMT, where methylation has been associated with Parkinson disease and glioblastoma, respectively) in which perinatal DNA methylation levels where linked to maternal periconceptual nutrition. One hundred 18 (11.6%) of the ME candidates overlapped with genes where DNA methylation correlated (r > 0.871; p < 0.055) with expression in the colon mucosa of 5 independent control children. Genes involved in homophilic cell adhesion (including cadherin-associated genes) and developmental processes were significantly overrepresented in association with MEs. Additional filtering of gene expression-correlated MEs defined 35 genes, associated with 2 or more CpG sites within a 10 kb genomic region, fulfilling the ME criteria. DNA methylation changes at a number of these genes have been linked to various forms of human disease, including cancers, such as asthma and acute myeloid leukemia (ALOX12), gastric cancer (EBF3), breast cancer (NAV1), colon cancer and acute lymphoid leukemia (KCNK15), Wilms tumor (protocadherin gene cluster; PCDHAs) and colorectal cancer (TCERG1L), suggesting a potential etiologic role for MEs in tumorigenesis and underscoring the possible developmental origins of these malignancies. The presented compendium of ME candidates may accelerate our understanding of the epigenetic origins of common human disorders.     

Engineered alignment in media equivalents: magnetic prealignment and mandrel compaction.

We predicted and measured the evolution of smooth muscle cell (SMC) orientation in media-equivalents (MEs) for four fabrication conditions (F-, M-, F+, M+) under Free or Mandrel compaction (F/M) with and without magnetic prealignment of the collagen fibrils in the circumferential direction (+/-). Mandrel compaction refers to SMC-induced compaction of the ME that is constrained by having a nonadhesive mandrel placed in the ME lumen. Predictions were made using our anisotropic biphasic theory (ABT) for tissue-equivalent mechanics. Successful prediction of trends of the SMC orientation data for all four fabrication cases was obtained: maintenance of the initial isotropic state for F-, loss of initial circumferential alignment for F+, development of circumferential alignment for M-, and enhancement of initial circumferential alignment for M+. These results suggest two mechanisms by which the presence of the mandrel leads to much greater mechanical stiffness in the circumferential direction reported for mandrel compacted MEs relative to free compacted MEs: (1) by inducing an increasing circumferential alignment of the SMC and collagen, and (2) by inducing a large stress on the SMC, resulting in secretion and accumulation of stiffening components.     

Salt-bridges in the microenvironment of stable protein structures

Salt-bridges (sb) play an important role in the folding and stability of proteins. This is deduced from the evaluation of net energy in the microenvironments (ME, residues that are 4 Å away from positive and negative partners of salt-bridge and interact with them). MEs act as a determinant of net-energy due to the intrinsic features in the sequence. The stability of extremophilic proteins is due to the presence of favorable residues at the ME without any unfavorable residues. We studied a dataset of four structures from the protein data bank (PDB) and a homology model (1HM5) to gain insights on this issue. Data shows that the presence of isolated charges and polar residues in the core of extremophilic proteins helps in the formation of stable salt-bridges with reduced desolvation. Thus, site-specific mutations with favorable residues at the ME will help to develop thermo stable proteins with strong salt bridges.     

Value of mucin detection in distinguishing mucoepidermoid carcinoma from Warthin's tumor on fine needle aspiration

OBJECTIVE: To examine the validity of the presence of mucin, utilizing a semiquantitative, statistical approach, as a criterion for distinguishing low to intermediate grade mucoepidermoid carcinoma (ME) from Warthin's tumor (WT). STUDY DESIGN: We selected histologically established fine needle aspiration (FNA) cases of ME (26) and WT (30) from a six-year period (January 1995-January 2001). Mucicarmine staining was performed on the FNA preparations. The amount of mucin detected was rated on a scale of 1-3, as follows: 1 = no mucin present, 2 = mucin present in the background and < 5% of tumor cells, and 3 = mucin present in the background and > or = 5% tumor cells. The scores for the 30 WTs and 26 MEs were tabulated and analyzed for statistical significance utilizing the Student t test. RESULTS: The mean mucin score for the 26 MEs was 1.81, SD .63. The mean mucin score for the 30 WTs was 1.52, SD .74. There was no statistically significant difference (P = .122) in the amount of mucin present between MEs and WTs in the 56 aspirate specimens examined. CONCLUSION: Based on the results of this study, the presence of extracellular or intracellular mucin in FNA specimens of salivary gland tumors may not be a reliable criterion for distinguishing WT from ME.     

植物CACTA转座子的研究进展

转座子是染色体上可移动的DNA序列,根据转座机制可将其分为：通过RNA中间体进行转座的逆转录座子（Retrotransposon）和通过DNA中间体进行转座的转座子（Transposon）。En／Spm家族转座子是后者中的一类,它的末端反向重复序列（Terminal inverted repeats,TIRs）具有保守的5个碱基CACTA,所以通常又称为CACTA转座子。除此之外,其靶位点一般为3bp的同向重复（Target site duplication,TSD）;亚末端区域分布着若干正向或反向的重复序列（Subterminal repeat,STR）。迄今为止,CACTA转座子仅发现于植物基因组。过去一直认为由于其相对保守的转座机制而拷贝较少,但最近研究发现,该因子多拷贝存在于某些禾本科植物基因组中。由于该家族在基因组中分布的广泛性,具有用作分子指纹的应用前景。本文就其结构、转座机制和应用前景等做一综述。     

Progress in Plant CACTA Elements

Transposable elements are DNA fragments that can insert new chromosomal locations. On the basis of the mechanism of transposition, transposable elements were divided into two classes. Class 1 elements were retroelements that used reverse transposase to transpose by an RNA intermediate. Class 2 elements or DNA transposons transposed directly from DNA to DNA. Of the Class 2 elements, CACTA superfamily, so far identified exclusively in plants and previously regarded as low-copy-transposon for the conserved mechanism of propagation, recently received considerable interest because of their increasing evidence reiterating their high copies in some plant genomes. This article aimed at outlining CACTA elements with regard to their structure, transposition, and utilization.     

The differential expression of ribosomal 18S RNA paralog genes from the chaetognath <Emphasis Type="Italic">Spadella cephaloptera</Emphasis>

Chaetognaths constitute a small marine phylum of approximately 120 species. Two classes of both 18S and 28S rRNA gene sequences have been evidenced in this phylum, even though significant intraindividual variation in the sequences of rRNA genes is unusual in animal genomes. These observations led to the hypothesis that this unusual genetic characteristic could play one or more physiological role(s). Using in situ hybridization on the frontal sections of the chaetognath Spadella cephaloptera, we found that the 18S Class I genes are expressed in the whole body, with a strong expression throughout the gut epithelium, whereas the expression of the 18S Class II genes is restricted to the oocytes. Our results could suggest that the paralog products of the 18S Class I genes are probably the "housekeeping" 18S rRNAs, whereas those of class II would only be essential in specific tissues. These results provide support for the idea that each type of 18S paralog is important for specific cellular functions and is under the control of selective factors.     

Ecrg4 Attenuates the Inflammatory Proliferative Response of Mucosal Epithelial Cells to Infection

We report an inverse relationship between expression of the orphan candidate tumor suppressor gene esophageal cancer related gene 4 (Ecrg4), and the mucosal epithelial cell response to infection in the middle ear (ME). First, we found constitutive Ecrg4 mRNA expression in normal, quiescent ME mucosa that was confirmed by immunostainning of mucosal epithelial cells and immunoblotting of tissue lysates for the 14 kDa Ecrg4 protein. Upon experimental ME infection, Ecrg4 gene expression rapidly decreased by over 80%, between 3 to 48 hrs, post infection. When explants of this infected mucosa were placed in culture and transduced with an adenovirus (AD) encoding Ecrg4 gene (ADEcrg4), the proliferative and migratory responses of mucosal cells were significantly inhibited. ADEcrg4 transduction of control explants from uninfected MEs had no effect on basal growth and migration. Over-expression of Ecrg4 in vivo, by pre-injecting MEs with ADEcrg4 48 hrs prior to infection, prevented the natural down-regulation of Ecrg4, reduced mucosal proliferation and prevented inflammatory cell infiltration normally observed after infection. Taken together, these data support a hypothesis that Ecrg4 plays a role in coordinating the inflammatory and proliferative response to infection of mucosal epithelium suggesting a possible mechanism for its putative anti-tumor activity.     

Contribution of maternal effect QTL to genetic architecture of early growth in mice

Existing approaches to characterizing quantitative trait loci (QTL) utilize a paradigm explicitly focused on the direct effects of genes, where phenotypic variation among individuals is mapped onto genetic variation of those individuals. For many characters, however, the genotype of the mother via its maternal effect accounts for a considerable portion of the genetically based variation in progeny phenotypes. Thus the focus on direct effect QTL may result in an insufficient or misleading characterization of genetic architecture due to the omission of the potentially important source of genetic variance contributed by maternal effects. We analyze the relative contribution of direct and maternal effect (ME) QTL to early growth in mice using a three-generation intercross of the Small (SM/J) and Large (LG/J) inbred mouse lineages. Using interval mapping and composite interval mapping, direct effect (DE) QTL for early growth (change in body mass during the interval from week 1 to 2) were detected in the F(2) generation of the intercross (n = 510), where no maternal genetic effect variance is present (all individuals are progeny of genetically identical F(1) mothers). ME QTL were detected by treating the phenotypes of cross-fostered F(3) pups as a characteristic of their nurse-dam (n = 168 dams with cross-fostered progeny). Five DE QTL, significant at a chromosome wide level (alpha = 0.05), were detected, with two significant at a genome wide level. FourME QTL significant at the chromosome wide level were detected, with three significant at the genome wide level. A model containing only DE QTL accounted for 11.8% of phenotypic variance, while a model containing only ME QTL accounted for 31.5% of the among litter variance in growth. There was no evidence for pleiotropy of DE and ME loci since there was no overlap between loci detected in these two analyses. Epistasis between all pairs of loci was analyzed for both DEs and MEs. Ten pairs of loci showed significant epistasis for MEs (alpha = 0.05 corrected for multiple comparisons) while four pairs showed significant epistasis for DEs on early growth.     

Nutrient broth/PEG200/TritonX114/Tween80/Chloroform microemulsion as a reservoir of solubilized sitosterol for biotransformation to androstenedione

Microemulsions (ME) can act as a reservoir of solubilized hydrophobic substrates. The biotransformation of hydrophobic sitosterol to androstenedione (AD) with MEs prepared from nutrient broth and PEG 200 (1:1) as aqueous phase, 40 g/l sitosterol dissolved in chloroform as organic phase, Triton X114 and Tween 80 (1:1) as surfactant phase, was investigated. The phase behavior of this system was studied for ten different ratios(w/w), 10:0, 9:1, 8:2, 7:3, 6:4, 5:5, 4:6, 3:7, 2:8, 1:9 and 0:10 of the organic phase and surfactant at 30 °C. A pseudoternary phase diagram was constructed to demarcate the region giving stable MEs. The maximum solubility of sitosterol in ME medium was observed to be 8 g/l, which is 3 orders of magnitude higher than the reported sitosterol solubility of 2–4 mg/l in aqueous medium. The ME medium was used for biotransformation studies and a comparative result has been reported. Transmission electron microscopy of cells grown in ME having oil, surfactant and aqueous phase in the ratio of 6:14:80 showed a weakened cell wall structure that permitted production of 465.86 mg/l AD.     

Disentangling prenatal and postnatal maternal genetic effects reveals persistent prenatal effects on offspring growth in mice

Mothers are often the most important determinant of traits expressed by their offspring. These "maternal effects" (MEs) are especially crucial in early development, but can also persist into adulthood. They have been shown to play a role in a diversity of evolutionary and ecological processes, especially when genetically based. Although the importance of MEs is becoming widely appreciated, we know little about their underlying genetic basis. We address the dearth of genetic data by providing a simple approach, using combined genotype information from parents and offspring, to identify "maternal genetic effects" (MGEs) contributing to natural variation in complex traits. Combined with experimental cross-fostering, our approach also allows for the separation of pre- and postnatal MGEs, providing rare insights into prenatal effects. Applying this approach to an experimental mouse population, we identified 13 ME loci affecting body weight, most of which (12/13) exhibited prenatal effects, and nearly half (6/13) exhibiting postnatal effects. MGEs contributed more to variation in body weight than the direct effects of the offsprings' own genotypes until mice reached adulthood, but continued to represent a major component of variation through adulthood. Prenatal effects always contributed more variation than postnatal effects, especially for those effects that persisted into adulthood. These results suggest that MGEs may be an important component of genetic architecture that is generally overlooked in studies focused on direct mapping from genotype to phenotype. Our approach can be used in both experimental and natural populations, providing a widely practicable means of expanding our understanding of MGEs.     

RNase T2 genes from rice and the evolution of secretory ribonucleases in plants

The plant RNase T2 family is divided into two different subfamilies. S-RNases are involved in rejection of self-pollen during the establishment of self-incompatibility in three plant families. S-like RNases, on the other hand, are not involved in self-incompatibility, and although gene expression studies point to a role in plant defense and phosphate recycling, their biological roles are less well understood. Although S-RNases have been subjects of many phylogenetic studies, few have included an extensive analysis of S-like RNases, and genome-wide analyses to determine the number of S-like RNases in fully sequenced plant genomes are missing. We characterized the eight RNase T2 genes present in the Oryza sativa genome; and we also identified the full complement of RNase T2 genes present in other fully sequenced plant genomes. Phylogenetics and gene expression analyses identified two classes among the S-like RNase subfamily. Class I genes show tissue specificity and stress regulation. Inactivation of RNase activity has occurred repeatedly throughout evolution. On the other hand, Class II seems to have conserved more ancestral characteristics; and, unlike other S-like RNases, genes in this class are conserved in all plant species analyzed and most are constitutively expressed. Our results suggest that gene duplication resulted in high diversification of Class I genes. Many of these genes are differentially expressed in response to stress, and we propose that protein characteristics, such as the increase in basic residues can have a defense role independent of RNase activity. On the other hand, constitutive expression and phylogenetic conservation suggest that Class II S-like RNases may have a housekeeping role.     

Mechanisms of stiffening and strengthening in media-equivalents fabricated using glycation

We have recently reported that glycation can be exploited to increase the circumferential tensile stiffness and ultimate tensile strength of media-equivalents (MEs) and increase their resistance to collagenolytic degradation, all without loss of cell viability (Girton et al., 1999). The glycated MEs were fabricated by entrapping high passage adult rat aorta SMCs in collagen gel made from pepsin-digested bovine dermal collagen, and incubated for up to 10 weeks in complete medium with 30 mM ribose added. We report here on experiments showing that ME compaction due to traction exerted by the SMCs with consequent alignment of collagen fibrils was necessary to realize the glycation-mediated stiffening and strengthening, but that synthesis of extracellular matrix constituents by these cells likely contributed little, even when 50 micrograms/ml ascorbate was added to the medium. These glycated MEs exhibited a compliance similar to arteries, but possessed less tensile strength and much less burst strength. MEs fabricated with low rather than high passage adult rat aorta SMCs possessed almost ten times greater tensile strength, suggesting that alternative SMCs sources and biopolymer gels may yield sufficient strength by compositional remodeling prior to implantation in addition to the structural remodeling (i.e., circumferential alignment) already obtained.     

Preparation and Evaluation of Microemulsion Systems Containing Salicylic Acid

Microemulsions (MEs) are clear, thermodynamically stable systems. They were used to solubilize drugs and to improve topical drug availability. Salicylic acid (SA) is a keratolytic agent used in topical products with antimicrobial actions. The objective of this work was to prepare and evaluate SA ME systems. Different concentrations of SA were incorporated in an ME base composed of isopropyl myristate, water, and Tween 80: propylene glycol in the ratio of 15:1. Three ME systems were prepared: S_2%, S_5%, and S_10% which contain 2%, 5%, and 10% of SA, respectively. Evaluation by examination under cross-polarizing microscope, measuring of percent transmittance, pH measurement, determination of the specific gravity, assessment of rheological properties, and accelerated stability study were carried out. The data showed that the addition of SA markedly affected the physical properties of the base. All systems were not affected by accelerated stability tests. Stability study for 6 months under ambient conditions was carried out for S_10%. No remarkable changes were recorded except a decrease in the viscosity value after 1 month. The results suggested that ME could be a suitable vehicle for topical application of different concentrations of SA.     

Mechanical efficiency of locomotion in females during different kinds of muscle action

The mechanical efficiencies (ME) of pure positive and pure negative work as well as of stretch-shortening cycle (SSC) exercise were investigated with a special sledge apparatus. The subjects were 20 young females who performed six different types of submaximal exercise: two of pure concentric exercise (positive work), two of pure eccentric exercise (negative work) and two SSC exercises. The work intensities were determined individually, from the recordings of distance obtained during a single maximal concentric exercise. Each exercise involved 60 muscle actions lasting a total of 3 min per testing condition. The MEs of pure positive work with intensities of 30% and 60% maximum (C30 and C60 respectively) were 15.5%, SD 2.6% and 14.3%, SD 1.9%, respectively. In pure negative work, when the dropping heights were 20 cm (E20) and 80 cm (E80), MEs were 28.4%, SD 6.9% and 47.9%, SD 10.1%, respectively. In SSC-exercise, the MEs during the positive phase of the take-off were 31.3%, SD 6.3% (E20/C90) and 35.0%, SD 7.0% (E80/C69). The total MEs in SSC-exercise were 29.1%, SD 4.0% (E20/C90) and 40.1%, SD 5.2% (E80/C60 x 100). In pure negative work, the increased stretching velocity increased the value of ME. In the concentric phase of SSC-exercise, the integrated electromyographic activity (iEMG) of vastus lateralis (VL) and vastus medialis (VM) muscles were lower (P less than 0.05) than in pure concentric work, when the mechanical work was the same (C60 vs E80/C60). During pure eccentric work, iEMGs were lower in comparison to the eccentric phase of SSC-exercise.(ABSTRACT TRUNCATED AT 250 WORDS)