Production of cloned calves by combination treatment of both donor cells and early cloned embryos with 5-aza-2/-deoxycytidine and trichostatin A

We previously reported that treatment of both donor cells and early cloned embryos with a combination of 0.01 μM 5-aza-2(/)-Deoxycytidine (5-aza-dC) and 0.05 μM trichostatin A (TSA) significantly improved development of cloned bovine embryos in vitro. In the present study, we investigated the effect of this combination treatment on the in vivo development potency and postnatal survivability of cloned calves. Blastocysts (77 and 82 blastocysts derived from untreated (control) and treated groups, respectively) were individually transferred to recipient cows. Relative to the control group, the combination treatment of both donor cells and early embryos with 5-aza-dC and TSA dramatically increased the cleavage rate (49.2 vs 63.6%, P < 0.05) at 24 h of culture, and blastocyst development rate on Days 6 and 7 of culture (18.8 vs 33.9% and 27.1 vs 38.5% respectively, P < 0.05). Although pregnancy rate did not differ 40 d after transfer, it was lower in the treated than control group 90 d after transfer (7.8 vs 29.3%, P < 0.05). In the control group, there were three calves born to 77 recipients (only two survived beyond 60 d), whereas in the treated group, 17 calves were born to 82 recipients, and 11 survived beyond 60 d. In conclusion, a combination treatment of donor cells and early cloned embryos with 5-aza-dC and TSA significantly enhanced development of somatic cell cloned bovine embryos in vivo; cloning efficiency (number of surviving calves at 60 d of birth/number of recipient cows) was increased from 2.6 to 13.4%.

The significance of neuroglobin in the brain

Since its discovery in 2000, neuroglobin (Nb) has been demonstrated to have an essential and conserved function in vertebrates with the consequential discovery of a neuroprotective role. Nb is a member of the globin superfamily and is predominantly expressed in neurons of the central and peripheral nervous system. Thorough studies have been performed to elucidate the molecular structure of Nb and its ligand binding characteristics. The precise physiological function and mechanism of action of Nb is beginning to be established, with a number of hypotheses having been put forward. While Nb shares an intrinsic affinity for low-molecular weight diatomic gases similar to other globins, the relatively low level of Nb expression in cerebral neurons places limitations on its potential to function as a reservoir for oxygen, especially during periods of acute ischemia. In vitro studies have suggested that the neuroprotective role of Nb may be due to its ability to scavenge reactive oxygen (ROS) and nitrogen (RNS) species. However other studies have proposed Nb as being part of a signalling chain that transmits the redox state of the cell that is protective against oxidative stress or that inhibits apoptosis. This review is intended to summarize the structural, genomic and functional data on neuroglobin to date, thereby providing perspectives for future research on these molecules that may have substantial biomedical implications.

Adaptive evolution of the mitochondrial ND6 gene in the domestic horse

Mitochondria play a crucial role in energy metabolism through oxidative phosphorylation. Organisms living at high altitudes are potentially influenced by oxygen deficits and cold temperatures. The severe environmental conditions can impact on metabolism and direct selection of mitochondrial DNA. As a wide-ranging animal, the domestic horse (Equus caballus) has developed various morphological and physiological characteristics for adapting to different altitudes. Thus, this is a good species for studying adaption to high altitudes at a molecular level. We sequenced the complete NADH dehydrogenase 6 gene (ND6) of 509 horses from 24 sampling locations. By comparative analysis of three horse populations living at different altitudes (>2200 m, 1200-1700 m, and <900 m), we found that the high-altitude population had the lowest genetic diversity and significant negative Tajima's D; both values declined with increasing elevation. Moreover, non-directional selection was identified for the ND6 gene by a tree-based relative ratio test (P = 0.007); the highest proportion of high-altitude horses was found distributed on the selected branches. We conclude that the high-altitude environment has directed adaptive evolution of the mitochondrial ND6 gene in the plateau horse.

Development in vitro and mitochondrial fate of interspecies cloned embryos

Although the technique of interspecies somatic cell nuclear transfer can be used to increase the population size of endangered mammals, the mitochondrial heteroplasmy in cloned embryos and animals makes this idea doubtful. In present study, goat-sheep cloned embryos were constructed by fusing goat foetal fibroblasts (GFFs) into sheep oocytes and then cultured in vitro to investigate the capability of sheep oocyte dedifferentiating GFF nucleus. Moreover, at each stage of 1- (immediately after fused), 2-, 4-, 8-, 16-cell, morula and blastocyst, the copy number of mtDNA from GFF and sheep oocyte was examined using real-time PCR. The results showed that: 7.4% of the fused cloned embryos can develop to the blastocyst stage; in the process of one cell to the morula stage, the copy number of two kinds of mtDNA was stable relatively; however, in the process of morula to the blastocyst stage, the decreasing in the copy number of GFF-derived mtDNA, while the increasing in sheep oocyte-derived, resulted in their ratio of decreasing sharply from 2.0 +/- 1.0% to 0.012 +/- 0.004%. This study demonstrates that: (i) the goat-sheep cloned embryos have the ability to develop to blastocyst in vitro; (ii) from the morula stage to the blastocyst stage of goat-sheep cloned embryos, goat derived mitochondria can be gradually replaced with those from sheep oocyte.

The effect of contact lens induced oedema on the accuracy of Goldmann tonometry in a mature population

AIM

To determine the effect of contact lens induced oedema on the accuracy of Goldmann tonometry measurements of intraocular pressure (IOP) in mature subjects.

METHODS

22 healthy subjects aged between 50 and 60 years were recruited. Corneal curvature, IOP, and central corneal thickness (CCT) were measured before and after two hours of monocular closed eye wear of a thick hydroxyethyl methacrylate (HEMA) contact lens. Measurements were then repeated at 20 minute intervals for one hour after lens removal.

RESULTS

Both CCT (+54.1 mum) and IOP (+2.7 mm Hg) increased significantly after lens wear (p<0.001, paired t test with Bonferroni correction). For the hour following lens removal, the measured IOP was correlated to the increase in CCT (r = 0.84, p<0.001), at a rate of 1.0 mm Hg/10 mum (95% confidence interval, 0.8 to 1.2 mm Hg/10 mum, linear mixed model analysis).

CONCLUSIONS

A relatively small increase in CCT from contact lens induced corneal oedema caused an overestimation error in Goldmann tonometry measurements of IOP in healthy mature subjects.

Role of interleukin (IL)-1 type 1 receptor in mycobacterial infection

It is important to gain a better understanding of IL-1-mediated signaling events in mycobacterial infection. In order to clarify the role of IL-1 receptor type 1 (IL-1 R1) in IL-1 R1, knockout (KO) mice were infected with either Mycobacterium tuberculosis H37Rv or Kurono strain by the respiratory route, and their ability to control mycobacterial growth, pulmonary granuloma formation, and cytokine mRNA expression was investigated. IL-1 R1 KO mice developed significantly larger (P< 0.01) granulomatous lesions with neutrophil infiltration in their lungs than wild-type mice did after infection with the M. tuberculosis Kurono strain. The number of mycobacterial colonies in lungs and spleen increased from five weeks post-infection. Interferon-y production by spleen cells was low in IL-1 R1 KO mice. It is concluded that the IL-1 R1 is essential for IL-1-mediated signaling events in mycobacterial infection.

Interaction of morin with CTMAB: aggregation and location in micellar

The aggregation and location of morin in CTMAB micellar solution was studied by light scattering spectra, electronic absorption spectra and pulsed FT NMR techniques. The difference in the light scattering property of morin with and without CTMAB proved that a large particle of the morin-CTMAB associate formed. Morin has a self-assembly tendency, but the assembly number is not high. With the increase of morin concentration, morin changed from a monomer to dimer. The hyperchromic and bathochromic effect of morin, with the increase in pH value or

Support vector machine approach for protein subcellular localization prediction

MOTIVATION

Subcellular localization is a key functional characteristic of proteins. A fully automatic and reliable prediction system for protein subcellular localization is needed, especially for the analysis of large-scale genome sequences.

RESULTS

In this paper, Support Vector Machine has been introduced to predict the subcellular localization of proteins from their amino acid compositions. The total prediction accuracies reach 91.4% for three subcellular locations in prokaryotic organisms and 79.4% for four locations in eukaryotic organisms. Predictions by our approach are robust to errors in the protein N-terminal sequences. This new approach provides superior prediction performance compared with existing algorithms based on amino acid composition and can be a complementary method to other existing methods based on sorting signals.

AVAILABILITY

A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

SUPPLEMENTARY INFORMATION

Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/.

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach

We have introduced a new method of protein secondary structure prediction which is based on the theory of support vector machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than that of traditional machine learning approaches, including neural networks.The first use of the SVM approach to predict protein secondary structure is described here. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of segment overlap accuracy SOV=76.2 % through sevenfold cross validation on a database of 513 non-homologous protein chains with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q(3) achieved 73.5 %, which is at least comparable to existing single prediction methods. Furthermore a useful "reliability index" for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.

Distinct topologies of mono- and decavanadate binding and photo-oxidative cleavage in the sarcoplasmic reticulum ATPase

UV irradiation of the sarcoplasmic reticulum (SR) ATPase in the presence of vanadate cleaves the enzyme at either of two different sites. Under conditions favoring the presence of monovanadate, and in the presence of Ca(2+), ADP, and Mg(2+), cleavage results in two fragments of 71- and 38-kDa electrophoretic mobility. On the other hand, under conditions permitting formation of decavanadate, and in the absence of Ca(2+) and ADP, cleavage results in two fragments of 88- and 21-kDa electrophoretic mobility. The amino terminus resulting from cleavage is blocked and resistant to Edman degradation. However, the initial photo-oxidation product can be reduced with NaB(3)H(4,) resulting in incorporation of radioactive (3)H label. Extensive digestion of the labeled protein with trypsin then yields labeled peptides that are specific for the each of the photo-oxidation conditions, and can be sequenced after purification. Collection of the Edman reaction fractional products reveals the radioactive label and demonstrates that Thr(353) is the residue oxidized by monovanadate at the phosphorylation site (i.e. Asp(351)). Correct positioning of monovanadate at the phosphorylation site requires binding of Mg(2+) and ADP to the Ca(2+)-dependent conformation of the enzyme. Subsequent hydrolytic cleavage is likely assisted by the neighboring Asp(601), and yields the 71- and 38-kDa fragments. On the other hand, Ser(186) (and possibly the following three residues: Val(187), Ile(188), and Lys(189)) is the residue that is photo-oxidized by decavanadate in the absence of ADP. Hydrolytic cleavage of the oxidized product at this site is likely assisted by neighboring acidic residues, and yields the 88- and 21-kDa fragments. The bound decavanadate, which we find to produce steric interference with TNP-AMP binding, must therefore extend to the A domain (i.e. small cytosolic loop) in order to oxidize Ser(186). This protein conformation is only obtained in the absence of Ca(2+).

Activity of an alcohol-based hand gel against human adeno-, rhino-, and rotaviruses using the fingerpad method

OBJECTIVE

To assess the activity against three non-enveloped viruses (an adeno-, a rhino- and a rotavirus) of a gel containing 60% ethanol, using experimentally contaminated thumb- and fingerpads of 12 panelists, as per standard procedure E-1838-96 of the American Society of Testing and Materials.

DESIGN

Each digit received 10 microL of the test virus suspension. The inoculum from the thumbs was eluted immediately with 990 microL of Earle's balanced salt solution (EBSS) to assess the amount of virus on each digit (0-minute control). The inoculum on the fingers was allowed to dry (20-25 minutes), and virus was eluted from two fingerpads to determine the loss in virus infectivity upon drying (baseline titer). Then the dried inoculum on randomly selected fingers was exposed to 1 mL of the test product or standard hard water (200-ppm calcium carbonate) for 20 seconds. The virus remaining was eluted with 1 mL of EBSS, titrated to determine the amounts eliminated, and compared to the baseline titer.

RESULTS

Each digit received at least 10(4) plaque-forming units of virus in 10 microL. The amounts of adeno-, rhino-, and rotaviruses surviving the drying were 30%, 75%, and 42%, respectively. The product reduced the infectivity titers of the three viruses by 3 to >4 log10 when compared to a reduction of < or =1 log10 for the hard-water rinse.

CONCLUSION

The level of virus reduction by gel was statistically significantly higher than that seen with the water control. Evidence for such activity against non-enveloped viruses supports further investigation of the benefits of this product.

GCIP, a novel human grap2 and cyclin D interacting protein, regulates E2F-mediated transcriptional activity

Regulation of mammalian cell growth and proliferation is governed through receptor-mediated signaling networks that ultimately converge on the cell cycle machinery. Adaptor proteins play essential roles in the formation of intracellular signaling complexes, relaying extracellular signals from the plasma membrane to the nucleus of a cell. The leukocyte-specific adaptor protein Grap2 is a central linker protein in immune cell signaling and activation. Using Grap2 as bait protein, we identified a novel human protein, GCIP (Grap2 cyclin-D interacting protein). We found that GCIP bound to Grap2 in both yeast two-hybrid assays and in mammalian cells through binding to the COOH-terminal unique domain and SH3 domain (designated QC domain) of Grap2. GCIP also associated with cyclin D both in vitro and in vivo. The expression of GCIP was found in all human tissues examined with the highest level of expression in the heart, muscle, peripheral blood leukocytes, and brain. Furthermore, phosphorylation of retinoblastoma protein by cyclin D-dependent protein kinase was reduced and E2F1-mediated transcription activity was inhibited in cells transfected with GCIP. High level expression of GCIP in terminally differentiated tissues and the inhibition of E2F1 transcription activation suggest that GCIP could play an important role in controlling cell differentiation and proliferation.

Characterization of calcium, nucleotide, phosphate, and vanadate bound states by derivatization of sarcoplasmic reticulum ATPase with ThioGlo1

Sarcoplasmic reticulum vesicles were incubated with the maleimide-directed probe ThioGlo1, resulting in ATPase inactivation. Reacted ThioGlo1, revealed by its enhanced fluorescence, was found to be associated with the cytosolic but not with the membrane-bound region of the ATPase. The dependence of inactivation on ThioGlo1 concentration suggests derivatization of approximately four residues per ATPase, of which Cys(364), Cys(498), and Cys(636) were identified in prominently fluorescent peptide fragments. These cysteines reside within the phosphorylation and nucleotide-binding region of the ATPase. Accordingly, protection is observed in the presence of ATP, 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-diphosphate (TNP-AMP), or an fluoroisothiocyanate label of Lys(515). Furthermore, protection is observed in the presence of vanadate (or decavanadate), but not in the presence of phosphate. Labeling occurs equally well in the presence or in the absence of Ca(2+) and thapsigargin, excluding a role of the E1-to-E2 transition in the protective effect of vanadate. It is concluded that protection by vanadate is due to formation of a pentacoordinated orthovanadate complex at the phosphorylation site, corresponding to a stable transition state analog of the phosphorylation reaction, with intermediate characteristics of the EP1 and EP2 states. The lack of protection by phosphate is attributed to instability of its complex with the enzyme (EP2). These findings are discussed with respect to different structural images obtained from diffraction studies of ATPase in the presence or in the absence of Ca(2+) and/or decavanadate (Ogawa et al., 1998, Biophys. J. 75:41-52).