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 SOD1G93A 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.

Spy1, a unique cell cycle regulator, alters viability in ALS motor neurons and cell lines in response to mutant SOD1-induced DNA damage.

Increasing evidence indicates that DNA damage and p53 activation play major roles in the pathological process of motor neuron death in amyotrophic lateral sclerosis (ALS). Human SpeedyA1 (Spy1), a member of the Speedy/Ringo family, enhances cell proliferation and promotes tumorigenesis. Further studies have demonstrated that Spy1 promotes cell survival and inhibits DNA damage-induced apoptosis. We showed that the Spy1 expression levels were substantially decreased in ALS motor neurons compared with wild-type controls both in vivo and in vitro by qRT-PCR, western blotting, and Immunoassay tests. In addition, we established that over-expression of human SOD1 mutant G93A led to a decreased expression of Spy1. Furthermore, DNA damage response was activated in SOD1G93A-transfected cells (mSOD1 cells). Moreover, decreased Spy1 expression reduced cell viability and further activated the DNA damage response in mSOD1 cells. In contrast, increased Spy1 expression improved cell viability and inhibited the DNA damage response in mSOD1 cells. These results suggest that Spy1 plays a protective role in ALS motor neurons. Importantly, these findings provide a novel direction for therapeutic options for patients with ALS as well as for trial designs, such as investigating the role of oncogenic proteins in ALS.

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.

Gene essentiality analysis based on DEG 10, an updated database of essential genes.

The database of essential genes (DEG, available at http://www.essentialgene.org), constructed in 2003, has been timely updated to harbor essential-gene records of bacteria, archaea, and eukaryotes. DEG 10, the current release, includes not only essential protein-coding genes determined by genome-wide gene essentiality screens but also essential noncoding RNAs, promoters, regulatory sequences, and replication origins. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools. Based on the analysis of DEG 10, we show that the percentage of essential genes in bacterial genomes exhibits an exponential decay with increasing genome sizes. The functions, ATP binding (GO:0005524), GTP binding (GO:0005525), and DNA-directed RNA polymerase activity (GO:0003899), are likely required for organisms across life domains.

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.

[Effects of performing pelvic lymph node dissection before versus after radical cystectomy].

OBJECTIVE: To explore the efficacies of extended pelvic lymph node dissection (e-PLND) before or after radical cystectomy (RC). METHODS: From January 2003 to January 2013, a total of 107 patients underwent e-PLND plus RC. And their relevant clinical data were reviewed. Their median age was (62 ± 10) years. The e-PLND were divided into 10 regions and 6 groups according to the anatomic sites. Forty-seven (43.9%) underwent RC after e-PLND (group A) and 60 (56.1%) had RC before e-PLND (group B). Two groups were compared for operative duration, numbers of lymph nodes removed, metastatic rates of lymph node, dissected lymph node positive rates and operative complications. The results were analyzed with Chi-square or Student's test. RESULTS: Clinicopathological characteristics were comparable for two groups (P > 0.05). The mean operative durations of e-PLND were similar in both groups ( (83 ± 27) vs (78 ± 24) min , P > 0.05). The mean operative durations of RC were significantly shorter in group A than those in group B ( (79 ± 41) vs (113 ± 44) min, P < 0.01) . The mean number of lymph nodes removed (25.5 ± 9.7 vs 29.0 ± 8.4) and the mean number of lymph nodes removed at internal iliac (5.7 ± 2.9 vs 7.2 ± 3.5) and presacral (1.3 ± 1.1 vs 2.5 ± 1.6) regions were significantly fewer in group A than those in group B (all P < 0.05). The metastatic rates of lymph node (34.0% (16/47) vs 31.7% (19/60)), dissected lymph node positive rates (9.0% (108/1197) vs 7.5% (130/1743)) and operative complications (23.4% (11/47) vs 20.0% (12/60)) were similar in both groups (all P > 0.05). CONCLUSION: RC is performed preferably after e-PLND, and internal iliac and presacral area should be dissected for additional lymph nodes after RC.

A proposal for a novel impact factor as an alternative to the JCR impact factor.

One disadvantage of the JCR impact factor, the most commonly used assessment tool for ranking and evaluating scientific journals, is its inability in distinguishing among different shapes of citation distribution curves, leading to unfair evaluation of journals in some cases. This paper aims to put forward an alternative impact factor (IF') that can properly reflect citation distributions. The two impact factors are linearly and positively correlated, and have roughly the same order of magnitude. Because of the ability of IF' in distinguishing among different shapes of citation distribution curves, IF' may properly reflect the academic performance of a scientific journal in a way that is different from the JCR impact factor with some unique features that reward journals with highly cited papers. Therefore, it is suggested that IF' could be used to complement the JCR impact factor.

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).

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.

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.

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.

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.

[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.