We describe methods for generating artificial transcription factors capable of up- or downregulating the expression of genes whose promoter regions contain the target DNA sequences. To accomplish this, we screened zinc fingers derived from sequences in the human genome and isolated 56 zinc fingers with diverse DNA-binding specificities. We used these zinc fingers as modular building blocks in the construction of novel, sequence-specific DNA-binding proteins. Fusion of these zinc-finger proteins with either a transcriptional activation or repression domain yielded potent transcriptional activators or repressors, respectively. These results show that the human genome encodes zinc fingers with diverse DNA-binding specificities and that these domains can be used to design sequence-specific DNA-binding proteins and artificial transcription factors.

Some of the previously reported clinical isolates of Elizabethkingia meningoseptica may be later named species of Elizabethkingia. We determined the accuracy of species identification (with two matrix-assisted laser desorption ionizationtime of flight mass spectrometry [MALDI-TOF MS] systems and the Vitek 2 GN card), relative prevalence of three Elizabethkingia spp. in clinical specimens, and antimicrobial susceptibility of the species identified by 16S rRNA gene sequencing. Specimens for culture were collected from patients in a university hospital in Seoul, South Korea, between 2009 and 2015. All 3 Elizabethkingia spp. were detected in patients; among the 86 isolates identified by 16S rRNA gene sequencing, 17 (19.8%) were E. meningoseptica, 18 (20.9%) were Elizabethkingia miricola, and 51 (59.3%) were Elizabethkingia anophelis. Only the MALDI-TOF Vitek MS system with an amended database correctly identified all of the isolates. The majority (76.7%) of the isolates were from the lower respiratory tract, and 8 (9.3%) were from blood. Over 90% of E. meningoseptica and E. anophelis isolates were susceptible to piperacillin-tazobactam and rifampin. In contrast, all E. miricola isolates were susceptible to fluoroquinolones except ciprofloxacin. Further studies are urgently needed to determine the optimal antimicrobial agents for the treatment of infections due to each individual Elizabethkingia species.KEYWORDS Elizabethkingia meningoseptica, Elizabethkingia miricola, Elizabethkingia anophelis, antimicrobial susceptibility, 16S rRNA gene sequencing E lizabethkingia species are aerobic, nonmotile, oxidase-positive, indole-positive, Gram-negative bacilli that do not ferment glucose. Elizabethkingia spp. can be found frequently in soil, freshwater, salt water, and in hospital environments (1). However, they do not normally exist in the human body. Elizabethkingia meningoseptica (formerly Chryseobacterium meningosepticum) has been a well-known human pathogen since its first description in a case of neonatal meningitis by Elizabeth O. King in 1959 (2). This organism was reported to cause various invasive infections in immunocompromised hosts and to be associated with nosocomial infections and outbreaks in intensive care units (ICUs) (3-5). It has been considered that the incidence of E. meningoseptica bacteremia has increased over the last decade (6). Two new species of Elizabethkingia, Elizabethkingia miricola and Elizabethkingia anophelis, were proposed in 2003 and 2011, respectively (7-9). Therefore, some of the previously reported clinical isolates of E. meningoseptica may be later named species of Elizabethkingia. The first

We have developed a method in which randomized libraries of zinc finger-containing artificial transcription factors are used to induce phenotypic variations in yeast and mammalian cells. By linking multiple zinc-finger domains together, we constructed more than 100,000 zinc-finger proteins with diverse DNA-binding specificities and fused each of them to either a transcription activation or repression domain. The resulting transcriptional regulatory proteins were expressed individually in cells, and the transfected cells were screened for various phenotypic changes, such as drug resistance, thermotolerance or osmotolerance in yeast, and differentiation in mammalian cells. Genes associated with the selected phenotypes were also identified. Our results show that randomized libraries of artificial transcription factors are useful tools for functional genomics and phenotypic engineering.

Normalization of mRNA levels using endogenous reference genes (ERGs) is critical for an accurate comparison of gene expression between different samples. Despite the popularity of traditional ERGs (tERGs) such as GAPDH and ACTB, their expression variability in different tissues or disease status has been reported. Here, we first selected candidate housekeeping genes (HKGs) using human gene expression data from different platforms including EST, SAGE, and microarray, and 13 novel ERGs (nERGs) (ARL8B, CTBP1, CUL1, DIMT1L, FBXW2, GPBP1, LUC7L2, OAZ1, PAPOLA, SPG21, TRIM27, UBQLN1, ZNF207) were further identified from these HKGs. The mean coefficient variation (CV) values of nERGs were significantly lower than those of tERGs and the expression level of most nERGs was relatively lower than high expressing tERGs in all dataset. The higher expression stability and lower expression levels of most nERGs were validated in 108 human samples including formalin-fixed paraffin-embedded (FFPE) tissues, frozen tissues and cell lines, through quantitative real-time RT-PCR (qRT-PCR). Furthermore, the optimal number of nERGs required for accurate normalization was as few as two, while four genes were required when using tERGs in FFPE tissues. Most nERGs identified in this study should be better reference genes than tERGs, based on their higher expression stability and fewer numbers needed for normalization when multiple ERGs are required.

The identification of novel tumor-specific proteins or antigens is of great importance for diagnostic and therapeutic applications in pancreatic cancer. Using oligonucleotide microarrays, we identified a broad spectrum of differentially expressed pancreatic cancerrelated genes. Of these, we selected an overexpressed expressed sequence taq and cloned a 721-bp full-length cDNA with an open reading frame of 196 amino acids. This novel gene was localized on the Homo sapiens 16p13.3 chromosomal locus, and its nucleotide sequence matched the Homo sapiens similar to common salivary protein 1 (LOC124220). We named the gene pancreatic adenocarcinoma up-regulated factor. The pancreatic adenocarcinoma up-regulated factor was secreted into the culture medium of pancreatic adenocarcinoma up-regulated factor-overexpressing Chinese hamster ovary cells, had an apparent molecular mass of ~25 kDa, and was N-glycosylated. The induction of pancreatic adenocarcinoma up-regulated factor in Chinese hamster ovary cells increased cell proliferation, migration, and invasion ability in vitro. Subcutaneous injection of mice with Chinese hamster ovary/pancreatic adenocarcinoma up-regulated factor cells resulted in 3.8-fold greater tumor sizes compared to Chinese hamster ovary/mock cells. Reverse transcription-polymerase chain reaction and western blotting with antirecombinant human pancreatic adenocarcinoma up-regulated factor antibodies confirmed that pancreatic adenocarcinoma up-regulated factor was highly expressed in six of eight pancreatic cancer cell lines. Immunohistochemical staining of human pancreatic cancer tissues also showed pancreatic adenocarcinoma up-regulated factor overexpression in the cytoplasm of cancer cells. Transfection with pancreatic adenocarcinoma up-regulated factor-specific small-interfering RNA reduced cancer cell migration and invasion in vitro. Treatment with antirecombinant human pancreatic adenocarcinoma up-regulated factor in vitro and in vivo reduced proliferation, migration, invasion, and tumorigenic ability. Collectively, our results suggest that pancreatic adenocarcinoma up-regulated factor is a novel secretory protein involved in pancreatic cancer progression and might be a potential target for the treatment of pancreatic cancer. (Cancer Sci 2009; 100: 828-836)

Background Anaerobic bacterial resistance trends may vary across regions or institutions. Regional susceptibility patterns are pivotal in the empirical treatment of anaerobic infections. We determined the antimicrobial resistance patterns of clinically important anaerobic bacteria, including recently named or renamed anaerobes. Methods A total of 521 non-duplicated clinical isolates of anaerobic bacteria were collected from a tertiary-care hospital in Korea between 2014 and 2016. Anaerobes were isolated from blood, body fluids, and abscess specimens. Each isolate was identified by conventional methods and by Bruker biotyper mass spectrometry (Bruker Daltonics, Leipzig, Germany) or VITEK matrix-assisted laser desorption ionization time-of-flight mass spectrometry (bioMérieux, Marcy-l'Étoile, France). Antimicrobial susceptibility was tested using the agar dilution method according to the CLSI guidelines. The following antimicrobials were tested: piperacillin-tazobactam, cefoxitin, cefotetan, imipenem, meropenem, clindamycin, moxifloxacin, chloramphenicol, tetracycline, and metronidazole. Results Most Bacteroides fragilis isolates were susceptible to piperacillin-tazobactam, imipenem, and meropenem. The non- fragilis Bacteroides group (including B. intestinalis , B. nordii , B. pyogenes , B. stercoris , B. salyersiae , and B. cellulosilyticus ) was resistant to meropenem (14%) and cefotetan (71%), and Parabacteroides distasonis was resistant to imipenem (11%) and cefotetan (95%). Overall, the Prevotella and Fusobacterium isolates were more susceptible to antimicrobial agents than the B. fragilis group isolates. Anaerobic gram-positive cocci exhibited various resistance rates to tetracycline (6–86%). Clostridioides difficile was highly resistant to penicillin, cefoxitin, imipenem, clindamycin, and moxifloxacin. Conclusions Piperacillin-tazobactam, cefoxitin, and carbapenems are highly active β-lactam agents against most anaerobes, including recently named or renamed species.

Adherent-invasive Escherichia coli (AIEC) has been reported as associated with the pathogenesis of inflammatory bowel disease (IBD). We aimed to investigate the characteristics of mucosa-associated E . coli and the clinical significance of AIEC in Korean IBD patients. E . coli strains were isolated from the mucosal tissues of 18 Crohn’s disease (CD) patients, 24 ulcerative colitis (UC) patients, and 9 healthy controls (HC). Adhesion, invasion, and survival assays were performed to evaluate phenotypic features of E . coli isolates and to identify AIEC. The presence of virulence genes and cytokine expression were examined using PCR. In addition, data on IBD-related hospitalization were collected. A total of 59 E . coli strains were isolated (25 from CD, 27 from UC, and 7 from HC). The average levels of adhesion, invasion, and survival were higher in E . coli strains from IBD patients than those from HC (adhesion: 1.65 vs. 0.71, p = 0.046; invasion: 1.68 vs. 0.52, p = 0.039; survival: 519.55 vs. 47.55, p = 0.363). Prevalence of AIEC in HC, CD and UC patients was 22.2%, 38.9% and 37.5%, respectively. E . coli isolates from IBD patients had various virulence genes and were associated with increased expression of TNF-α and IL-17. IBD-related hospitalization within 3 years was 18.8% in patients with AIEC and 11.5% in patients without AIEC. E . coli strains from IBD patients showed high levels of adhesion, invasion, and survival. AIEC strains were identified in both CD and UC patients at a similar rate. AIEC may be associated with sustaining inflammation in the pre-existing inflammatory mucosa.

BackgroundInvestigation on incidence and mortality of anaerobic bacteremia (AB) is clinically relevant in spite of its infrequent occurrence and not often explored, which report varies according to period and institutions. Therefore, it is necessary to analyze the incidence and risk factors related to mortality and assess clinical outcomes of AB in current aspect.Materials and MethodsCharacteristics of AB patients and anaerobic bacteria from blood culture at a university hospital in 2012 were reviewed retrospectively. The correlation between risk factors and 28-day patient mortality was analyzed.ResultsA total of 70 non-duplicated anaerobic bacteria were isolated from blood of 70 bacteremia patients in 2012. The history of cardiovascular disease as host's risk factor was statistically significant (P = 0.0344) in univariate and multivariate analysis. Although the inappropriate therapy was not statistically significant in univariate and multivariate analysis, the survival rate of bacteremia was significantly worse in patients who had inappropriate therapy compared with those underwent appropriate therapy (hazard ratio, 5.4; 95% confidence interval, 1.7–6.9; P = 0.004). The most frequently isolated organism was Bacteroides fragilis (32 isolates, 46%), followed by Bacteroides thetaiotaomicron (10, 14%), and non-perfringens Clostridium (7, 10%).ConclusionThe incidence of AB in 2012 was 2.3% (number of AB patients per 100 positive blood culture patients) and the mortality rate in patients with clinically significant AB was 21.4%. In addition, AB was frequently noted in patients having malignancy and the survival rate of AB was significantly worse in patients who received inappropriate therapy compared with those underwent appropriate therapy.