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.

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.

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.

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.

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.

DeOri: a database of eukaryotic DNA replication origins.

SUMMARY: DNA replication, a central event for cell proliferation, is the basis of biological inheritance. The identification of replication origins helps to reveal the mechanism of the regulation of DNA replication. However, only few eukaryotic replication origins were characterized not long ago; nevertheless, recent genome-wide approaches have boosted the number of mapped replication origins. To gain a comprehensive understanding of the nature of eukaryotic replication origins, we have constructed a Database of Eukaryotic ORIs (DeOri), which contains all the eukaryotic ones identified by genome-wide analyses currently available. A total of 16 145 eukaryotic replication origins have been collected from 6 eukaryotic organisms in which genome-wide studies have been performed, the replication-origin numbers being 433, 7489, 1543, 148, 348 and 6184 for humans, mice, Arabidopsis thaliana, Kluyveromyces lactis, Schizosaccharomyces pombe and Drosophila melanogaster, respectively. AVAILABILITY: Database of Eukaryotic ORIs (DeOri) can be accessed from http://tubic.tju.edu.cn/deori/

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).

[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.

[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.

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.

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.

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.

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.

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.

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/.

DoriC: a database of oriC regions in bacterial genomes.

UNLABELLED: 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.

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.