[Mechanical circulatory support combined with immunomodulation treatment for patients with fulminant myocarditis: a single-center real-world study]

Objective: To investigate the relationship between the mechanical circulatory support (MCS) combined with immunomodulation and the prognosis of patients with fulminant myocarditis. Methods: This is a retrospective study. A total of 88 patients with fulminant myocarditis admitted to Dongguan Kanghua hospital from Aug. 2008 to Dec. 2020 were included. Medical histories, results of laboratory tests, treatment regimens and clinical outcomes of these patients during their hospitalization were collected from the medical record system. According to the treatment methods, the patients were divided into MCS+immunomodulation group (38 cases), MCS group (20 cases) and traditional treatment group (30 cases). Patients in the MCS+immunomodulation group received intra-aortic balloon pump (IABP) or IABP combined with extracorporeal membrane oxygenation (ECMO) and immunoglobulin or glucocorticoid. Patients in the MCS group only received mechanical circulatory support. Patients in the traditional treatment group received neither mechanical circulatory support nor immunomodulatory therapy, and only used vasoactive drugs and cardiotonic drugs. The in-hospital mortality and length of stay were compared among the three groups. Results: A total of 88 patients with fulminant myocarditis aged (35.0±10.8) years were included, and there were 46 males (52.3%). The mortality of MCS+immunomodulation group (7.9% (3/38) vs. 56.7% (17/30), P=0.001 2) and MCS group (30.0% (6/20) vs. 56.7% (17/30), P=0.002 8) were lower than that of traditional treatment group. Compared with the MCS group, the in-hospital mortality in the MCS+immunomodulation group was lower (P=0.005 4). The most common cause of death was multiple organ dysfunction syndrome (MODS). The constituent ratios of death in MCS+immunomodulation group, MCS group and traditional treatment group were 3/3, 4/6 and 12/17, respectively. The incidence of MODS in the MCS group (20% (4/20)) and the traditional treatment group (40% (12/30)) was significantly higher than that in the MCS+immunomodulation group (7.9% (3/38)) (both P<0.01). In discharged patients, the hospitalization time of MCS+immunomodulation group was shorter than that of traditional treatment group ((13.4±5.5)d vs. (18.5±7.4)d, P<0.05) and MCS group ((13.4±5.5)d vs. (16.9±8.5)d, P<0.05). Conclusion: MCS combined with immunomodulatory therapy is associated with lower in-hospital mortality and shorter hospital stay in patients with fulminant myocarditis.

DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools

Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.

Wild-type p53-induced phosphatase 1 down-regulation promotes apoptosis by activating the DNA damage-response pathway in amyotrophic lateral sclerosis

Accumulation of DNA damage has been detected in the spinal cord of patients as well as in the G93A mouse model of amyotrophic lateral sclerosis (ALS). Wild-type p53-induced phosphatase 1 (Wip1) is a p53-inducible serine/threonine phosphatase that terminates DNA-damage responses via dephosphorylation of DNA-damage response proteins, namely ataxia-telangiectasia mutated (ATM) kinase, checkpoint kinase 2, and p53, thus enhancing cell proliferation. However, the role of Wip1, DNA-damage responses, and their interaction in ALS development remains to be elucidated. Here, we showed that Wip1 expression levels were substantially decreased in ALS motor neurons compared with wild-type controls both in vivo and in vitro. The DNA-damage response was activated in superoxide dismutase 1 (SOD1) ^G93A-transfected cells. However, increased expression of Wip1 improved cell viability and inhibited the DNA-damage response in mutated SOD1^G93A cells. Further studies demonstrated that decreased Wip1 expression reduced cell viability and further activated the DNA-damage response in chronic H₂O₂-treated NSC34 cells. In contrast, Wip1 promoted cell survival and suppressed DNA damage-induced apoptosis during persistent DNA damage conditions. Over-expression of Wip1 in the central nervous system (CNS) can delay the onset of disease symptoms, extended the survival, decreased MN loss improved motor function and inhibit the DNA-damage response in SOD1 G93A mice. Furthermore, homeodomain-interacting protein kinase 2 (HIPK2) promoted the degradation of Wip1 via the ubiquitin-proteasome system during chronic stress. These findings indicate that persistent accumulation of DNA damage and subsequent chronic activation of the downstream DNA damage-response ATM and p53 pro-apoptotic signaling pathways may trigger neuronal dysfunction and neuronal death in ALS. Wip1 may play a protective role by targeting the DNA-damage response in ALS motor neurons. Importantly, these findings provide a novel direction for therapeutic options for patients with ALS.

Overexpression of miR-101-2 in donor cells improves the early development of Holstein cow somatic cell nuclear transfer embryos

Accumulating studies have suggested that microRNA play a part in regulating multiple cellular processes, such as cell proliferation, apoptosis, the cell cycle, and embryo development. This study explored the effects of miR-101-2 on donor cell physiological status and the development of Holstein cow somatic cell nuclear transfer (SCNT) embryos in vitro. Holstein cow bovine fetal fibroblasts (BFF) overexpressing miR-101-2 were used as donor cells to perform SCNT; then, cleavage rate, blastocyst rate, inner cell mass-to-trophectoderm ratio, and the expression of some development- and apoptosis-related genes in different groups were analyzed. The miR-101-2 suppressed the expression of inhibitor of growth protein 3 (ING3) at mRNA and protein levels, expedited cell proliferation, and decreased apoptosis in BFF, suggesting that ING3, a target gene of miR-101-2, is a potential player in this process. Moreover, by utilizing donor cells overexpressing miR-101-2, the development of bovine SCNT embryos in vitro was significantly enhanced; the apoptotic rate in SCNT blastocysts was reduced, and the inner cell mass-to-trophectoderm ratio and SOX2, POU5F1, and BCL2L1 expression significantly increased, whereas BAX and ING3 expression decreased. Collectively, these findings suggest that miR-101-2 promotes BFF proliferation and vitality, reduces their apoptosis, and improves the early development of SCNT embryos.

Protective effects of trehalose on frozen-thawed ovarian granulosa cells of cattle

In this study, trehalose was investigated for its cryoprotective effects on ovarian granulosa cells (bGCs) of cattle. Five concentrations of trehalose at 0, 0.2, 0.4, 0.6 and 0.8 mol/L were added to the cryopreservation medium of bGCs, and the effects on the quality of frozen-thawed bGCs were assessed. The results indicate that the use of cryopreservation medium containing 0.2 and 0.4 mol/L of trehalose resulted in a greater rate of bGC viability compared to those of other groups (P<0.05). Culturing with trehalose at 0.2 and 0.4 mol/L increased 17β- estradiol (E₂)and decreased progesterone (P₄)production (P < 0.05) in post-thawed bGCs. Compared with the control group, the intracellular Ca²⁺ concentrations of frozen-thawed bGCs were less in all treatment groups (P<0.05), and the least Ca²⁺ concentration was observed in the group containing 0.4 mol/L trehalose. The plasma membrane potentials of frozen-thawed bGCs were greater in the groups with 0.2 and 0.4 mol/L trehalose, and the group treated with 0.4 mol/L trehalose had the greatest membrane potential in comparison to other groups (P < 0.05). The relative abundance of the CYP19 mRNA in frozen-thawed bGCs was greater in the groups containing 0.2, 0.4 and 0.6 mol/L trehalose, and relative abundances of FSHR and BCL2 mRNA were greater in the group of bGCs treated with 0.2 mol/L trehalose (P<0.05). Trehalose treatment at 0.4, 0.6 and 0.8 mol/L had an inhibitory effect on BAX gene transcription in frozen-thawed bGCs (P<0.05). In summary, trehalose exhibited a greater cryoprotective effect on bGCs than basic cryopreservation medium.

[Establishment and evaluation of a new method for determining hemodynamics of pulmonary hypertension rats]

Objective: By evaluating the hemodynamic parameters such as cardiac output (CO), right ventricular pressure (RVP), pulmonary artery pressure (PAP) and total pulmonary resistance index (TPRI) in pulmonary hypertension rat model, we established a more comprehensive hemodynamic evaluation system, which objectively evaluated the severity of disease and exercise tolerance in rats with pulmonary hypertension. Methods: SD rats were randomly divided into a control group and a model group with 5 rats in each group. The model group was intraperitoneally injected with SU5416 (20 mg/kg) and placed in an oxygen chamber at a 10% oxygen concentration for 21 days and then placed in a normoxic environment for 14 days. After modeling, rats were anesthetized and mechanically ventilated. The operator cut the skin along the right paraxial line, detached and ligated the intercostal artery, and then cut off the 3 and 4 ribs, exposing the heart and freeing aortic root about 0.2 cm. The flowmeter probe was set in the dissected aortic segment, and real-time recording time, blood flow waveforms, cardiac output were calculated accordingly. Then the needle attached to the baroreceptor was inserted into the right ventricle and the system acquired the right ventricular time-pressure waveform. After the waveform stabilized for about 30 seconds, the end of the cannula was sent to the pulmonary artery trunk through the entrance of the pulmonary artery to record the time-pressure curve of the pulmonary artery. Results: RVSP, PASP, PADP and mPAP in the model group were significantly higher than those of the control group [ RVSP(23.4±5.4) mmHg, 1 mmHg=0.133 kPa vs (56.4±13.0) mmHg, PASP (22.8±4.4) mmHg vs (58.5±14.9) mmHg, PADP (9.7±1.9) mmHg vs (30.3±7.0) mmHg, mPAP (14.1±2.7) mmHg vs (41.9±8.0) mmHg, all P<0.05 ]. Compared with the control group, the cardiac index in the model group was significantly lower [ CI (0.54±0.08) ml·min(-1)·g(-1) vs (0.40±0.09) ml·min(-1)·g(-1,) P=0.02 ]. Furthermore, compared with the control group, pulmonary vascular resistance index was significantly increased in the model group[PVRI (0.27±0.03) mmHg·ml(-1)·min(-1)·kg(-1) vs (0.06±0.01) mmHg·ml(-1)·min(-1)·kg(-1,) P<0.05]. The pathological results also showed that the middle part of pulmonary arterioles in the model group had muscular hypertrophy and muscular pulmonary arterioles, and even plexiform lesions. Conclusion: In this study, we established a new method that simultaneously determined several hemodynamic parameters such as RVSP, PASP, PADP, CO, CI and PVRI, which provided a more comprehensive assessment of hemodynamic changes in pulmonary hypertension rat models.

Fisetin Exerts Antioxidant and Neuroprotective Effects in Multiple Mutant hSOD1 Models of Amyotrophic Lateral Sclerosis by Activating ERK

Oxidative stress exhibits a central role in the course of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease commonly found to include a copper/zinc superoxide dismutase (SOD1) gene mutation. Fisetin, a natural antioxidant, has shown benefits in varied neurodegenerative diseases. The possible effect of fisetin in ALS has not been clarified as of yet. We investigated whether fisetin affected mutant hSOD1 ALS models. Three different hSOD1-related mutant models were used: Drosophila expressing mutant hSOD1^G85R, hSOD1^G93A NSC34 cells, and transgenic mice. Fisetin treatment provided neuroprotection as demonstrated by an improved survival rate, attenuated motor impairment, reduced ROS damage and regulated redox homeostasis compared with those in controls. Furthermore, fisetin increased the expression of phosphorylated ERK and upregulated antioxidant factors, which were reversed by MEK/ERK inhibition. Finally, fisetin reduced the levels of both mutant and wild-type hSOD1 in vivo and in vitro, as well as the levels of detergent-insoluble hSOD1 proteins. The results indicate that fisetin protects cells from ROS damage and improves the pathological behaviors caused by oxidative stress in disease models related to SOD1 gene mutations probably by activating ERK, thereby providing a potential treatment for ALS.

"Perfect" designer chromosome V and behavior of a ring derivative

Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis. We designed and de novo synthesized 536,024-base pair chromosome synV in the "Build-A-Genome China" course. We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.

[Primary culture and functional identification of distal pulmonary artery smooth muscle cells in mice]

Objective: To establish a method of isolation and primary culture of mice distal pulmonary artery smooth muscle cells (PASMCs) and identify the functional properties. Methods: PASMCs were harvested from the distal pulmonary artery (PA) tissue of mice by enzymatic digestion of collagenaseⅠand papain; and the growth characteristics were observed under inverted microscope and identified by Immunofluorescence technique. Effects on the intracellular calcium ion concentration of distal PASMCs were detected by Fura-2-AM fluorescent probe tracer under a fluorescence microscope in Krebs solution containing clopiazonic acid (CPA) and nifedipin (Nif). Results: PASMCs density reached approximately to 80% in a typical valley-peak-like shape after 6 days. Cell α-smooth muscle actin (α-SMA) immunofluorescence identified that 95% of the cultured cells were PASMCs. More than 95% PASMCs responded well to calcium-potassium Krebs solution (potassium ion concentration of 60 mmol/L) and showed a rapid increase in basal [Ca(2+) ](i) after 1 minute's perfusion (Δ[Ca(2+) ](i)>50), which demonstrated that the voltage-dependent calcium channels (VDCC) of distal PASMCs were in good function; after the perfusion of calcium Krebs, calcium-free/calcium-Krebs containing CPA and Nif, distal PASMCs showed two typical peaks, indicated the full function of store-operated calcium channel (SOCC) in distal PASMCs. Conclusion: This experiment successfully established a stable and reliable mice distal PASMCs model and the study of pulmonary vascular diseases could benefit from its higher purity and better functional condition.

Downregulation of Homer1b/c in SOD1 G93A Models of ALS: A Novel Mechanism of Neuroprotective Effect of Lithium and Valproic Acid

Background: Mutations in the Cu/Zn superoxide dismutase (SOD1) gene have been linked to amyotrophic lateral sclerosis (ALS). However, the molecular mechanisms have not been elucidated yet. Homer family protein Homer1b/c is expressed widely in the central nervous system and plays important roles in neurological diseases. In this study, we explored whether Homer1b/c was involved in SOD1 mutation-linked ALS. Results: In vitro studies showed that the SOD1 G93A mutation induced an increase of Homer1b/c expression at both the mRNA and protein levels in NSC34 cells. Knockdown of Homer1b/c expression using its short interfering RNA (siRNA) (si-Homer1) protected SOD1 G93A NSC34 cells from apoptosis. The expressions of Homer1b/c and apoptosis-related protein Bax were also suppressed, while Bcl-2 was increased by lithium and valproic acid (VPA) in SOD1 G93A NSC34 cells. In vivo, both the mRNA and protein levels of Homer1b/c were increased significantly in the lumbar spinal cord in SOD1 G93A transgenic mice compared with wild type (WT) mice. Moreover, lithium and VPA treatment suppressed the expression of Homer1b/c in SOD1 G93A mice. Conclusion: The suppression of SOD1 G93A mutation-induced Homer1b/c upregulation protected ALS against neuronal apoptosis, which is a novel mechanism of the neuroprotective effect of lithium and VPA. This study provides new insights into pathogenesis and treatment of ALS.

Differential response in levels of high-density lipoprotein cholesterol to one-year metformin treatment in prediabetic patients by race/ethnicity

Background

As a first-line diabetes drug that is widely prescribed around the world, metformin has been demonstrated to be effective in reducing microvascular risk, in addition to lowering glucose levels. Specifically, metformin use has been shown to be associated with improved lipid profiles, such as increased levels of high-density lipoprotein cholesterol (HDL-C). However, no study has been performed to examine the differential response in HDL-C levels to metformin treatment by race/ethnicity.

Methods

Here, based on a re-analysis of the data from the Diabetes Prevention Program, which involved pre-diabetic participants receiving 850 mg of metformin twice daily, we compared the lipid profile changes following the metformin use. The participants were composed of 602 Whites, 221 African Americans (AAs) and 162 Hispanics.

Results

We found that the one-year metformin treatment resulted in a significant increase in HDL-C levels in Whites (p = 0.002) and AAs (p = 0.016), but not in Hispanics. Consistently, both Whites (p = 0.018) and AAs (p = 0.020) had more pronounced changes in HDL-C levels than Hispanics following metformin treatment.

Conclusion

This result suggests a notion that Whites and AAs are more responsive than Hispanics to one-year metformin use in HDL-C level changes, and that racial and ethnic identity is a factor to consider when interpreting the effects of metformin treatment on lipid profiles.

A reduction in both visceral and subcutaneous fats contributes to increased adiponectin by lifestyle intervention in the Diabetes Prevention Program

AIMS

Adiponectin, an insulin-sensitizing adipokine, confers protection against type 2 diabetes. Although adiponectin is secreted exclusively from fat, contributions of visceral adipose tissue (VAT) versus subcutaneous adipose tissue (SAT) to adiponectin levels have not been fully understood. We aimed to examine correlations between changes in VAT and SAT volumes and changes in adiponectin levels.

METHODS

Here, we have investigated the correlations between ΔVAT and ΔSAT with Δadiponectin in participants of the Diabetes Prevention Program, a clinical trial investigating the effects of lifestyle changes and metformin versus placebo on the rate of developing type 2 diabetes. Data on VAT and SAT volumes, measured by computed tomography, and on adiponectin levels at both baseline and 1-year follow-up were available in 321 men and 626 women.

RESULTS

In men, Δadiponectin was highly significantly correlated with both ΔSAT (r s  = -0.329) and ΔVAT (r s  = -0.413). Likewise, in women, Δadiponectin was correlated with both ΔSAT (r s  = -0.294) and ΔVAT (r s  = -0.348). In the lifestyle arm, Δadiponectin remained highly significantly correlated with ΔSAT and ΔVAT in men (r s  = -0.399 and r s  = -0.460, respectively), and in women (r s  = -0.372 and r s  = -0.396, respectively), with P < 0.001 for all above correlations.

CONCLUSIONS

We conclude that for both men and women, adiponectin changes are highly significantly correlated with changes in both SAT and VAT and that exercise- and weight-loss-induced reduction in both SAT and VAT contributes to the increased adiponectin.

Exome sequencing identifies novel ApoB loss-of-function mutations causing hypobetalipoproteinemia in type 1 diabetes

AIM

Diabetic patients commonly suffer from disturbances in production and clearance of plasma lipoproteins, known as diabetic dyslipidemia, resulting in an increased risk of coronary heart disease. The study aimed to examine the cause of hypobetalipoproteinemia in two patients with type 1 diabetes.

METHODS

The Diabetes Control and Complications Trial (DCCT) is a study demonstrating that intensive blood glucose control delays the onset and progression of type 1 diabetes complications. Hypobetalipoproteinemia was present in two DCCT subjects, IDs 1427 and 1078, whose LDL-C levels were 36 and 28 mg/dL, respectively, and triglyceride levels were 20 and 28 mg/dL, respectively. We performed exome sequencing on genomic DNA from the two patients with hypobetalipoproteinemia.

RESULTS

The subjects 1427 and 1078 had heterozygous loss-of-function mutations in the gene apolipoprotein B (ApoB), and these mutations resulted in premature stop codons at amino acid 1333 (ApoB-29) and 3680 (ApoB-81), respectively. Indeed, the plasma ApoB level of subject 1427 (19 mg/dL) was the lowest and that of subject 1078 (26 mg/dL) was the second to the lowest among all the 1,441 DCCT participants. Sequencing genomic DNA of family members showed that probands 1427 and 1078 inherited the mutations from the father and the mother, respectively.

CONCLUSIONS

The identification of ApoB loss-of-function mutations in type 1 diabetic patients presents innovative cases to study the interaction between hypobetalipoproteinemia and insulin deficiency.

Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes

DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/.

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements

The combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. DEG 10, a new release of the Database of Essential Genes (available at http://www.essentialgene.org), has been developed to accommodate these quantitative and qualitative advancements. In addition to increasing the number of bacterial and archaeal essential genes determined by genome-wide gene essentiality screens, DEG 10 also harbors essential noncoding RNAs, promoters, regulatory sequences and replication origins. These essential genomic elements are determined not only in vitro, but also in vivo, under diverse conditions including those for survival, pathogenesis and antibiotic resistance. We have developed customizable BLAST tools that allow users to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annotated or unannotated genomes. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools.

Chronopharmacokinetics of puerarin in diabetic rats

Puerarin injection has been widely used for clinic treatment of diabetes recently. To assess the relationship between the administration time of puerarin and the blood concentration of puerarin as well as its pharmacokinetic parameters, the diabetic rat model was used in current study. The rats were randomly divided into morning and evening groups according to the administration time. After the puerarin injection, blood glucose was tested in order to know whether the efficiency of puerarin was influenced by its concentration and pharmacokinetic parameters. Our results show that the average concentration of puerarin in the evening group is significantly higher than that in the morning group. The numbers of t_1/2α, t_1/2β, CL and AUC_(0-∞) are significantly different between the morning and evening groups. The blood glucose level in the evening group was lower than that in the morning group. The speed of its onset is higher and the blood glucose level declines much more significantly in the evening group. These findings suggest that the concentration and pharmacokinetic parameters of puerarin affect its efficiency in diabetic rats. Therefore, it might be better to give puerarin in evening than in the morning for the mellitus treatment.

The h'-index, effectively improving the h-index based on the citation distribution

Background

Although being a simple and effective index that has been widely used to evaluate academic output of scientists, the h-index suffers from drawbacks. One critical disadvantage is that only h-squared citations can be inferred from the h-index, which completely ignores excess and h-tail citations, leading to unfair and inaccurate evaluations in many cases.

Methodology /Principal Findings

To solve this problem, I propose the h’-index, in which h-squared, excess and h-tail citations are all considered. Based on the citation data of the 100 most prolific economists, comparing to h-index, the h’-index shows better correlation with indices of total-citation number and citations per publication, which, although relatively reliable and widely used, do not carry the information of the citation distribution. In contrast, the h’-index possesses the ability to discriminate the shapes of citation distributions, thus leading to more accurate evaluation.

Conclusions /Significance

The h’-index improves the h-index, as well as indices of total-citation number and citations per publication, by possessing the ability to discriminate shapes of citation distribution, thus making the h’-index a better single-number index for evaluating scientific output in a way that is fairer and more reasonable.

Pharmacokinetic interaction between scutellarin and valsartan in rats

Scutellarin is the main effective constituent of breviscapine, a flavonoid mixture isolated from the dried whole plant of Erigeron breviscapus (Vant.) Hand-Mazz, and valsartan is used as an antihypertensive drug. These two drugs have already been clinically used together to treat diabetic nephropathy (DN) in China, and the combined medications showed some enhanced protection against DN. The aim of this study is to investigate the potential pharmacokinetic interaction between scutellarin and valsartan in rats. Breviscapine injection (20 mg x kg(-1), i.v.) and valsartan (15 mg x kg-, i.g.), either alone or together were given to 18 male Sprague-Dawley rats. Concentrations of scutellarin and valsartan were quantified by HPLC, and pharmacokinetic parameters were calculated by non-compartmental methods. We found that the pharmacokinetic parameters of scutellarin altered significantly after co-administration of oral valsartan. The plasma clearance (CL(p)) and the bile clearance (CL(b)) of scutellarin were reduced significantly in the presence of valsartan. After oral administration of valsartan with or without intravenous scutellarin, however, the pharmacokinetic parameters of valsartan were comparable. In conclusion, our data suggests that the concurrent use of valsartan reduces the biliary excretion of scutellarin, and this may be due to the inhibitory effect of valsartan on the biliary excretion of scutellarin mediated by Mrp2 (Multidrug resistance-associated protein 2).

A novel triangle mapping technique to study the h-index based citation distribution

The h-index has received wide attention in recent years. The area under the citation function is divided by the h-index into three parts, representing h-squared, excess and h-tail citations. The h-index by itself does not carry information for excess and h-tail citations, which can play an even more dominant role than h-index in determining the citation curve, and therefore it is necessary to examine the relations among them. A triangle mapping technique is proposed here to map the three percentages of these citations onto a point within a regular triangle. By viewing the distribution of mapping points, shapes of the citation functions can be studied in a perceivable form. As an example, the distribution of the mapping points for 100 most prolific economists is studied by this technique.

Comparison of journal self-citation rates between some Chinese and non-Chinese international journals

Background

The past 3 decades have witnessed a boost in science development in China; in parallel, more and more Chinese scientific journals are indexed by the Journal Citation Reports issued by Thomson Reuters (SCI). Evaluation of the performance of these Chinese SCI journals is necessary and helpful to improve their quality. This study aimed to evaluate these journals by calculating various journal self-citation rates, which are important parameters influencing a journal impact factor.

Methodology/Principal Findings

We defined three journal self-citation rates, and studied these rates for 99 Chinese scientific journals, almost exhausting all Chinese SCI journals currently available. Likewise, we selected 99 non-Chinese international (abbreviated as ‘world’) journals, with each being in the same JCR subject category and having similar impact factors as their Chinese counterparts. Generally, Chinese journals tended to be higher in all the three self-citation rates than world journal counterparts. Particularly, a few Chinese scientific journals had much higher self-citation rates.

Conclusions/Significance

Our results show that generally Chinese scientific journals have higher self-citation rates than those of world journals. Consequently, Chinese scientific journals tend to have lower visibility and are more isolated in the relevant fields. Considering the fact that sciences are rapidly developing in China and so are Chinese scientific journals, we expect that the differences of journal self-citation rates between Chinese and world scientific journals will gradually disappear in the future. Some suggestions to solve the problems are presented.

The significance of fragile histidine triad protein as a molecular prognostic marker of bladder urothelial carcinoma

OBJECTIVES

The role and clinical significance of fragile histidine triad (FHIT) gene in the pathogenesis of bladder urothelial carcinoma (UC) and the potential of Fhit protein as a prognostic biomarker for UC were investigated.

METHODS

FHIT expression was determined according to semiquantitative immunohistochemical staining for Fhit protein levels in normal bladder and bladder UC tissues. Associations between FHIT expression, clinicopathological features and survival were evaluated.

RESULTS

This study evaluated 42 cases of normal bladder and 125 cases of bladder UC; bladder UC cases had a median follow-up of 53.5 months. Immuno histochemistry showed that 95.2% of normal cases and 47.2% of bladder UC cases, respectively, were positive for Fhit protein; this difference was statistically significant. There was a significant association between negative FHIT expression in bladder UC and advanced tumour stage, high pathological grade, large tumour size, tumour recurrence and reduced survival time, but no association with age, gender, tumour number or tumour shape.

CONCLUSIONS

The FHIT gene may have an important role in the pathogenesis of bladder UC and was expressed at lower levels in bladder UC compared with normal bladder tissue. Using Fhit protein as a biomarker could provide important information about patient prognosis.

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

Replication of chromosomes is one of the central events in the cell cycle. Chromosome replication begins at specific sites, called origins of replication (oriCs), for all three domains of life. However, the origins of replication still remain unknown in a considerably large number of bacterial and archaeal genomes completely sequenced so far. The availability of increasing complete bacterial and archaeal genomes has created challenges and opportunities for identification of their oriCs in silico, as well as in vivo. Based on the Z-curve theory, we have developed a web-based system Ori-Finder to predict oriCs in bacterial genomes with high accuracy and reliability by taking advantage of comparative genomics, and the predicted oriC regions have been organized into an online database DoriC, which is publicly available at http://tubic.tju.edu.cn/doric/ since 2007. Five years after we constructed DoriC, the database has significant advances over the number of bacterial genomes, increasing about 4-fold. Additionally, oriC regions in archaeal genomes identified by in vivo experiments, as well as in silico analyses, have also been added to the database. Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively.

[Expression of PIM-1 in prostate cancer tissue and its relationship with PSA recurrence]

OBJECTIVE

To explore the expression of the PIM-1 protein in prostate cancer tissue and its relationship with PSA recurrence.

METHODS

We used the immunohistochemical SP method to detect the expression of the PIM-1 protein in the prostate tissues of 68 cases of prostate cancer (PCa) and 37 cases of benign prostatic hyperplasia (BPH).

RESULTS

The positive rate of the PIM-1 protein expression was 67.65% (46/68) in the PCa tissue, significantly higher than 40.54% (15/37) in the BPH tissue (P<0.05). Its positive rates in PCa Gleason scores 6, 7 and 8-10 were 33.33% (7/21), 77.5% (21/28) and 94.74% (18/19), respectively, with significant between-group differences (P<0.05), and those in stages I , II, III and IV of PCa were 47.62%, 53.85%, 73.33% and 94.74%, respectively. Kaplan-Meier analysis of the results of a 36-month follow-up showed the ratios of PIM-1 expression to PSA recurrence and non-recurrence were 10/22 (45.45%) and 36/46 (78.26%), respectively, with statistically significant differences (P<0.05).

CONCLUSION

PIM-1 protein expression in PCa tissue is closely related to the Gleason score and clinical stage of PCa and PSA recurrence, which suggests that the PIM-1 gene plays an important role in PCa evolution and progression, and may be an indicator for the prognosis of PCa.

Promoter methylation of H-cadherin is a potential biomarker in patients with bladder transitional cell carcinoma

OBJECTIVES

H-cadherin, functions as a tumor suppressor, is frequently silenced by promoter methylation in human cancers. The aim of this study was to evaluate the feasibility of using H-cadherin methylation in tumor tissues as a potential biomarker in patients with bladder transitional cell carcinoma (TCC).

MATERIALS AND METHODS

We examined the methylation status of H-cadherin in 133 primary bladder TCC samples and 43 normal bladder epithelial tissues using methylation-specific polymerase chain reaction (MSP) and then analyzed the associations between H-cadherin methylation and clinicopathologic features as well as patients' outcome.

RESULTS

H-cadherin methylation was detected in 47 (35.3%) bladder TCC samples, but not found in controls (P = 0.0000). Moreover, H-cadherin methylation was significantly associated with advanced stage (P = 0.0006), high grade (P = 0.0165), larger tumor size (P = 0.0225), tumor recurrence (P = 0.0106), and poor prognosis (P = 0.0000). In addition, multivariate analysis indicated that H-cadherin methylation is independently associated with poor outcome and had a relative risk of death of 3.832 (P = 0.0071, 95% confidence interval: 1.443-10.176).

CONCLUSIONS

The results suggest that H-cadherin methylation may be used as a potential biomarker for the malignancy of bladder TCC and as an independent prognostic biomarker in patients with bladder TCC.

Functionality of essential genes drives gene strand-bias in bacterial genomes

Essential genes, indispensable genes for an organism's survival, encode functions that are considered a foundation of life. Based on those experimentally determined for 10 bacteria, we find that essential genes are more preferentially situated at the leading strand than at the lagging strand, for all the 10 genomes studied, confirming previous findings based on either smaller datasets or putatively assigned ones by homology search. Furthermore, we find that rather than all essential genes, only those with the COG functional category of information storage and process (J, K and L), and subcategories D (cell cycle control), M (cell wall biogenesis), O (posttranslational modification), C (energy production and conversion), G (carbohydrate transport and metabolism), E (amino acid transport and metabolism) and F (nucleotide transport and metabolism) are preferentially situated at the leading strand. In contrast, the strand-bias for essential genes in other COG functional subcategories is not statistically significant. These results suggest that the remarkable strand-bias of the distribution of essential genes is mainly relevant to the aforementioned functionalities, which, therefore, likely play a key role in shaping the gene strand-bias in bacterial genomes.

The e-index, complementing the h-index for excess citations

Background

The h-index has already been used by major citation databases to evaluate the academic performance of individual scientists. Although effective and simple, the h-index suffers from some drawbacks that limit its use in accurately and fairly comparing the scientific output of different researchers. These drawbacks include information loss and low resolution: the former refers to the fact that in addition to h² citations for papers in the h-core, excess citations are completely ignored, whereas the latter means that it is common for a group of researchers to have an identical h-index.

Methodology/Principal Findings

To solve these problems, I here propose the e-index, where e² represents the ignored excess citations, in addition to the h² citations for h-core papers. Citation information can be completely depicted by using the h-index together with the e-index, which are independent of each other. Some other h-type indices, such as a and R, are h-dependent, have information redundancy with h, and therefore, when used together with h, mask the real differences in excess citations of different researchers.

Conclusions/Significance

Although simple, the e-index is a necessary h-index complement, especially for evaluating highly cited scientists or for precisely comparing the scientific output of a group of scientists having an identical h-index.

Gene essentiality analysis based on DEG, a database of essential genes

Essential genes are the genes that are indispensable for the survival of an organism. The genome-scale identification of essential genes has been performed in various organisms, and we consequently constructed DEG, a Database that contains currently available essential genes. Here we analyzed functional distributions of essential genes in DEG, and found that some essential-gene functions are even conserved between the prokaryote (bacteria) and the eukaryote (yeast), e.g., genes involved in information storage and processing are overrepresented, whereas those involved in metabolism are underrepresented in essential genes compared with non-essential ones. In bacteria, species specificity in functional distribution of essential genes is mainly due to those involved in cellular processes. Furthermore, within the category of information storage and processing, function of translation, ribosomal structure, and biogenesis are predominant in essential genes. Finally, some potential pitfalls for analyzing gene essentiality based on DEG are discussed.

Prediction of replication time zones at single nucleotide resolution in the human genome

The human genome is structured at multiple levels: it is organized into a series of replication time zones, and meanwhile it is composed of isochores. Accumulating evidence suggests a match between these two genome features. Based on newly developed software GC-Profile, we obtained a complete coverage of the human genome by 3198 isochores with boundaries at single nucleotide resolution. Interestingly, the experimentally confirmed replication timing sites in the regions of 1p36.1, 6p21.32, 17q11.2 and 22q12.1 nearly all coincide with the determined isochore boundaries. The precise boundaries of the 3198 isochores are available via the website: http://tubic.tju.edu.cn/isomap/.

Origins of replication in Sorangium cellulosum and Microcystis aeruginosa

The genome of Sorangium cellulosum has recently been completely sequenced, and it is the largest bacterial genome sequenced so far. In their report, Schneiker et al. (in Complete genome sequence of the myxobacterium Sorangium cellulosum, Nat. Biotechnol., 2007, 25, 1281–1289) concluded that ‘In the absence of the GC-skew inversion typically seen at the replication origin of bacterial chromosomes, it was not possible to discern the location of oriC’. In addition, the complete genome of Microcystis aeruginosa NIES-843 has also been recently sequenced, and in this report, Kaneko et al. (in Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843, DNA Res., 2007, 14, 247–256) concluded that ‘there was no characteristic pattern, according to GC skew analysis’. Therefore, oriC locations of the above genomes remain unsolved. Using Ori-Finder, a recently developed computer program, in both genomes, we have identified candidate oriC regions that have almost all sequence hallmarks of bacterial oriCs, such as asymmetrical nucleotide distributions, being adjacent to the dnaN gene, and containing DnaA boxes and repeat elements.

Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes

BACKGROUND

Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes.

RESULTS

We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats.

CONCLUSION

A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes.

Greglist: a database listing potential G-quadruplex regulated genes

The double helix is a conformation that genomic DNA usually assumes; under certain conditions, however, guanine-rich DNA sequences can form a four-stranded structure, G-quadruplex, which is found to play a role in regulating gene expression. Indeed, it has been demonstrated that the G-quadruplex formed in the c-MYC promoter suppresses its transcriptional activity. Recent studies suggest that G-quadruplex motifs (GQMs) are enriched in human gene promoters. To facilitate the research of G-quadruplex, we have constructed Greglist, a database listing potentially G-quadruplex regulated genes. Greglist harbors genes that contain promoter GQMs from genomes of various species, including humans, mice, rats and chickens. Many important genes are found to contain previously unreported promoter GQMs, such as ATM, BAD, AKT1, LEPR, UCP1, APOE, DKK1, WT1, WEE1, WNT1 and CLOCK. Furthermore, we find that not only protein coding genes, 126 human microRNAs also contain promoter GQMs. Greglist therefore provides candidates for further studying G-quadruplex functions and is freely available at http://tubic.tju.edu.cn/greglist.

DoriC: a database of oriC regions in bacterial genomes

Replication origins (oriCs) of bacterial genomes currently available in GenBank have been predicted by using a systematic method comprising the Z-curve analysis for nucleotide distribution asymmetry, DnaA box distribution, genes adjacent to candidate oriCs and phylogenetic relationships. These oriCs are organized into a MySQL database, DoriC, which provides extensive information and graphical views of the oriC regions. In addition, users can Blast a query sequence or even a whole genome against DoriC to find a homologous one. DoriC will be updated timely and the latest version is DoriC 1.8, in which oriCs of 425 genomes (468 chromosomes) are identified.

AVAILABILITY

DoriC can be accessed from http://tubic.tju.edu.cn/doric/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at http://tubic.tju.edu.cn/doric/supplementary.htm.

GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences

In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website . In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.

Isochore structures in the chicken genome

The availability of the complete chicken genome sequence provides an unprecedented opportunity to study the global genome organization at the sequence level. Delineating compositionally homogeneous G + C domains in DNA sequences can provide much insight into the understanding of the organization and biological functions of the chicken genome. A new segmentation algorithm, which is simple and fast, has been proposed to partition a given genome or DNA sequence into compositionally distinct domains. By applying the new segmentation algorithm to the draft chicken genome sequence, the mosaic organization of the chicken genome can be confirmed at the sequence level. It is shown herein that the chicken genome is also characterized by a mosaic structure of isochores, long DNA segments that are fairly homogeneous in the G + C content. Consequently, 25 isochores longer than 2 Mb (megabases) have been identified in the chicken genome. These isochores have a fairly homogeneous G + C content and often correspond to meaningful biological units. With the aid of the technique of cumulative GC profile, we proposed an intuitive picture to display the distribution of segmentation points. The relationships between G + C content and the distributions of genes (CpG islands, and other genomic elements) were analyzed in a perceivable manner. The cumulative GC profile, equipped with the new segmentation algorithm, would be an appropriate starting point for analyzing the isochore structures of higher eukaryotic genomes.

The impact of comparative genomics on infectious disease research

The past decade has witnessed a revolution in infectious disease research, fuelled by the accumulation of a huge amount of DNA sequence data. The avalanche of genome sequence information has largely promoted the development of comparative genomics, which exploits available genome sequences to perform either inter- or intra-species comparisons of bacterial genome contents, or performs comparisons between the human genome and those of other organisms. This review aims to summarize how comparative genomics is being extensively used in infectious disease research, such as in the studies to identify virulence determinants, antimicrobial drug targets, vaccine candidates and new markers for diagnostics. These applications hold considerable promise for alleviating the burden of infectious diseases in the coming years.

ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

Background

It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This paper puts forward an alternative approach for viral and phage gene-finding to improve the quality of annotations, particularly for newly sequenced genomes.

Results

The new system ZCURVE_V has been run for 979 viral and 212 phage genomes, respectively, and satisfactory results are obtained. To have a fair comparison with the currently available software of similar function, GeneMark, a total of 30 viral genomes that have not been annotated by GeneMark are selected to be tested. Consequently, the average specificity of both systems is well matched, however the average sensitivity of ZCURVE_V for smaller viral genomes (< 100 kb), which constitute the main parts of viral genomes sequenced so far, is higher than that of GeneMark. Additionally, for the genome of Amsacta moorei entomopoxvirus, probably with the lowest genomic GC content among the sequenced organisms, the accuracy of ZCURVE_V is much better than that of GeneMark, because the later predicts hundreds of false-positive genes. ZCURVE_V is also used to analyze well-studied genomes, such as HIV-1, HBV and SARS-CoV. Accordingly, the performance of ZCURVE_V is generally better than that of GeneMark. Finally, ZCURVE_V may be downloaded and run locally, particularly facilitating its utilization, whereas GeneMark is not downloadable. Based on the above comparison, it is suggested that ZCURVE_V may serve as a preferred gene-finding tool for viral and phage genomes newly sequenced. However, it is also shown that the joint application of both systems, ZCURVE_V and GeneMark, leads to better gene-finding results. The system ZCURVE_V is freely available at: .

Conclusion

ZCURVE_V may serve as a preferred gene-finding tool used for viral and phage genomes, especially for anonymous viral and phage genomes newly sequenced.

Coronavirus phylogeny based on a geometric approach

A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the Z-curve representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the three-dimensional Z-curves. The Z-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the Z-curve, respectively. Although some information is lost due to the approximate description of the Z-curve, the phylogenetic tree constructed based on these parameters is consistent with those of previous analyses. The present method has the merits of simplicity and intuitiveness, but it is still in its premature stage. Because the phylogenetic relationships are inferred from the whole genome, instead of some individual genes, the present method represents a new direction of phylogeny study in the post-genome era.

Segmentation algorithm for DNA sequences

A new measure, to quantify the difference between two probability distributions, called the quadratic divergence, has been proposed. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains is put forward. The new algorithm has been applied to segment the 24 human chromosome sequences, and the boundaries of isochores for each chromosome were obtained. Compared with the results obtained by using the entropic segmentation algorithm based on the Jensen-Shannon divergence, both algorithms resulted in all identical coordinates of segmentation points. An explanation of the equivalence of the two segmentation algorithms is presented. The new algorithm has a number of advantages. Particularly, it is much simpler and faster than the entropy-based method. Therefore, the new algorithm is more suitable for analyzing long genome sequences, such as human and other newly sequenced eukaryotic genome sequences.

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1

The 2694 ORFs originally annotated as potential genes in the genome of Aeropyrum pernix can be categorized into three clusters (A, B, C), according to their nucleotide composition at three codon positions. Coding potential was found to be responsible for the phenomenon of three clusters in a 9-dimensional space derived from the nucleotide composition of ORFs: ORFs assigned to cluster A are coding ones, while those assigned to clusters B and C are non-coding ORFs. A "codingness" index called the AZ score is defined based on a clustering method used to recognize protein-coding genes in the A. pernix genome. The criterion for a coding or non-coding ORF is based on the AZ score. ORFs with AZ > 0 or AZ < 0 are coding or non-coding, respectively. Consequently, 620 out of 632 ORFs with putative functions based on the original annotation are contained in cluster A, which have positive AZ scores. In addition, all 29 ORFs encoding putative or conserved proteins newly added in RefSeq annotation also have positive AZ scores. Accordingly, the number of re-recognized protein-coding genes in the A. pernix genome is 1610, which is significantly less than 2694 in the original annotation and also much less than 1841 in the RefSeq annotation curated by NCBI staff. Annotation information of re-recognized genes and their AZ scores are available at: http://tubic.tju.edu.cn/Aper/.

Genomic islands in the Corynebacterium efficiens genome

Corynebacterium efficiens is a gram-positive nonpathogenic bacterium which can grow and produce glutamate at 40 degrees C or above. By using the cumulative GC profile method, we have identified four genomic islands which have many unifying genomic island-specific features in the C. efficiens genome. The presence of the gene encoding an aspartate kinase in a genomic island helps explain the unexpected low thermal stability of this enzyme; i.e., the adaptive mutations have not occurred extensively due to the recent horizontal gene transfer.

Identification of replication origins in archaeal genomes based on the Z-curve method

The Z-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both the Z-curve and the given DNA sequence can be uniquely reconstructed from the other. We employed Z-curve analysis to identify one replication origin in the Methanocaldococcus jannaschii genome, two replication origins in the Halobacterium species NRC-1 genome and one replication origin in the Methanosarcina mazei genome. One of the predicted replication origins of Halobacterium species NRC-1 is the same as a replication origin later identified by in vivo experiments. The Z-curve analysis of the Sulfolobus solfataricus P2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of the Z-curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of the Aeropyrum pernix K1, Methanococcus maripaludis S2, Picrophilus torridus DSM 9790 and Pyrobaculum aerophilum str. IM2 genomes.

Isochore structures in the mouse genome

The distribution of the G+C content in the mouse genome has been studied using a windowless technique. We have found that: (i). Abrupt variations of the G+C content from a GC-rich region to a GC-poor region, and vice versa, occur frequently at some sites along the sequence of the mouse genome. (ii). Long domains with relatively homogeneous G+C content (isochores) exist, which usually have sharp boundaries. Consequently, 28 isochores longer than 1 Mb have been identified in the mouse genome. A homogeneity index was used to quantify the variations of the G+C content within isochores. The precise boundaries, sizes, and G+C contents of these isochores have been determined. The windowless technique for the G+C content computation was also used to analyze the DNA sequence containing the mouse MHC region, which has a GC-poor isochore. This isochore is located at the central part of the sequence with boundaries at 468459 and 812716 bp, where the sequence is extended from the centromeric end to the telomeric end. In addition, the analysis of a segment of the rat genome shows that the rat genome also has clear isochore structures.

GS-Finder: a program to find bacterial gene start sites with a self-training method

In this paper, a self-training method is proposed to recognize translation start sites in bacterial genomes without a prior knowledge of rRNA in the genomes concerned. Many features with biological meanings are incorporated, including mononucleotide distribution patterns near the start codon, the start codon itself, the coding potential and the distance from the most-left start codon to the start codon. The proposed method correctly predicts 92% of the translation start sites of 195 experimentally confirmed Escherichia coli CDSs, 96% of 58 reliable Bacillus subtilis CDSs and 82% of 140 reliable Synechocystis CDSs. Moreover, the self-training method presented might also be used to relocate the translation start sites of putative CDSs of genomes, which are predicted by gene-finding programs. After post-processing by the method presented, the improvement of gene start prediction of some gene-finding programs is remarkable, e.g., the accuracy of gene start prediction of Glimmer 2.02 increases from 63 to 91% for 832 E. coli reliable CDSs. An open source computer program to implement the method, GS-Finder, is freely available for academic purposes from http://tubic.tju.edu.cn/GS-Finder/.