A 72 × 60 Angle-Sensitive SPAD Imaging Array for Lens-less FLIM.

We present a 72 × 60, angle-sensitive single photon avalanche diode (A-SPAD) array for lens-less 3D fluorescence lifetime imaging. An A-SPAD pixel consists of (1) a SPAD to provide precise photon arrival time where a time-resolved operation is utilized to avoid stimulus-induced saturation, and (2) integrated diffraction gratings on top of the SPAD to extract incident angles of the incoming light. The combination enables mapping of fluorescent sources with different lifetimes in 3D space down to micrometer scale. Futhermore, the chip presented herein integrates pixel-level counters to reduce output data-rate and to enable a precise timing control. The array is implemented in standard 180 nm complementary metal-oxide-semiconductor (CMOS) technology and characterized without any post-processing.

Preparation of Tunable (BaSrMg)O for Oxygen Chemisorption: Formation Mechanism and Characterization.

Composition-tunable single-phase three-component alkaline earth oxide of (BaSrMg)O was prepared based on the consecutive precipitation and thermal decomposition of (BaSrMg)CO3. First, the single-phase (BaSrMg)CO3 was coprecipitated via ion self-assembly, phase-transformation, and agglomeration. The element composition of (BaSrMg)CO3 could be simply tuned by the composition of the reactants. Then, (BaSrMg)CO3 was converted to (BaSrMg)O under an H2 atmosphere at 750 °C. This (BaSrMg)O showed fast chemisorption-desorption responses with oxygen chemisorption rate: t80 = 3.9 min and desorption rate: t80 = 14 min and a high thermal stability for the redox reaction of BaO-BaO2. In addition, the chemisorption capacity of (BaSrMg)O (4.39% Sr composition) is ∼1.92 mmol/g, which is much higher than the chemisorption capacity of BaO/MgO at 1.75 mmol/g (Jin et al., Ind. Eng. Chem. Res., 2005, 44, 2942), while the transient oxygen pressure for the redox reaction of (BaSrMg)O (4.39% Sr composition) was significantly enhanced from 76 to 135 mmHg due to the inclusion of Sr in (BaSrMg)O. The transient oxygen pressure could be further improved via adjusting the Sr composition in (BaSrMg)O. Consequently, the tunable (BaSrMg)O has a high potential as a chemisorbent for the industrial application of oxygen separation.

Unveiling the Mechanisms Underlying the Immunotherapeutic Potential of Gene-miRNA and Drugs in Head and Neck Cancer.

Head and neck cancer ranks as the sixth-most common malignancy worldwide, characterized by high mortality and recurrence rates. Research studies indicate that molecular diagnostics play a crucial role in the early detection and prognostic evaluation of these diseases. This study aimed to identify potential biomarkers for head and neck cancer and elucidate their interactions with miRNAs and possible therapeutic drugs. Four drivers, namely, FN1, IL1A, COL1A1, and MMP9, were identified using network biology and machine learning approaches. Gene set variation analysis (GSVA) showed that these genes were significantly involved in different biological processes and pathways, including coagulation, UV-response-down, apoptosis, NOTCH signaling, Wnt-beta catenin, and other signal pathways. The diagnostic value of these hub genes was validated using receiver operating characteristic (ROC) curves. The top interactive miRNAs, including miR-128-3p, miR-218-5p, miR-214-3p, miR-124-3p, miR-129-2-3p, and miR-1-3p, targeted the key genes. Furthermore, the interaction between the key genes and drugs was also identified. In summary, the key genes and miRNAs or drugs reported in this study might provide valuable information for potential biomarkers to increase the prognosis and diagnosis of head and neck cancer.

Stable, chronic in-vivo recordings from a fully wireless subdural-contained 65,536-electrode brain-computer interface device.

Minimally invasive, high-bandwidth brain-computer-interface (BCI) devices can revolutionize human applications. With orders-of-magnitude improvements in volumetric efficiency over other BCI technologies, we developed a 50-µm-thick, mechanically flexible micro-electrocorticography (µECoG) BCI, integrating 256×256 electrodes, signal processing, data telemetry, and wireless powering on a single complementary metal-oxide-semiconductor (CMOS) substrate containing 65,536 recording and 16,384 stimulation channels, from which we can simultaneously record up to 1024 channels at a given time. Fully implanted below the dura, our chip is wirelessly powered, communicating bi-directionally with an external relay station outside the body. We demonstrated chronic, reliable recordings for up to two weeks in pigs and up to two months in behaving non-human primates from somatosensory, motor, and visual cortices, decoding brain signals at high spatiotemporal resolution.

Comparative sequence analysis of a multidrug-resistant plasmid from Aeromonas hydrophila.

Aeromonas hydrophila is a pathogenic bacterium that has been implicated in fish, animal, and human disease. Recently, a multidrug resistance (MDR) plasmid, pR148, was isolated from A. hydrophila obtained from a tilapia (Oreochromis niloticus) farm in Thailand. pR148 is a 165,906-bp circular plasmid containing 147 coding regions showing highest similarity to pNDM-1_Dok1, an MDR plasmid isolated from a human pathogen. pR148 was also very similar to other IncA/C plasmids isolated from humans, animals, food, and fish. pR148 contains a mercuric resistance operon and encodes the complete set of genes for the type 4 secretion system. pR148 encodes a Tn21 type transposon. This transposon contains the drug resistance genes qacH, bla(OXA-10), aadA1, and sul1 in a class 1 integron; tetA and tetR in transposon Tn1721; and catA2 and a duplicate sul1 in a locus showing 100% similarity to IncU plasmids isolated from fish. The bla(OXA-10) and aadA1 genes showed 100% similarity to those from the Acinetobacter baumannii AYE genome. The similarity of pR148 to a human pathogen-derived plasmid indicates that the plasmids were either transferred between different genera or that they are derived from a common origin. Previous studies have shown that IncA/C plasmids retain a conserved backbone, while the accessory region points to lateral gene transfer. These observations point out the dangers of indiscriminate use of antibiotics in humans and in animals and the necessity of understanding how drug resistance determinants are disseminated and transferred.

Complete genome sequence of the bacteriophages ECBP1 and ECBP2 isolated from two different Escherichia coli strains.

Escherichia coli is recognized as one of the most abundant avian bacterial pathogens. In this study, we report the sequencing by the traditional Sanger method of ECBP1 and ECBP2: bacteriophages that infected two different E. coli strains which might be used as therapeutic agents in combination with alternative antibiotics.

wksl3, a New biocontrol agent for Salmonella enterica serovars enteritidis and typhimurium in foods: characterization, application, sequence analysis, and oral acute toxicity study.

Of the Salmonella enterica serovars, S. Enteritidis and S. Typhimurium are responsible for most of the Salmonella outbreaks implicated in the consumption of contaminated foods in the Republic of Korea. Because of the widespread occurrence of antimicrobial-resistant Salmonella in foods and food processing environments, bacteriophages have recently surfaced as an alternative biocontrol tool. In this study, we isolated a virulent bacteriophage (wksl3) that could specifically infect S. Enteritidis, S. Typhimurium, and several additional serovars. Transmission electron microscopy revealed that phage wksl3 belongs to the family Siphoviridae. Complete genome sequence analysis and bioinformatic analysis revealed that the DNA of phage wksl3 is composed of 42,766 bp with 64 open reading frames. Since it does not encode any phage lysogeny factors, toxins, pathogen-related genes, or food-borne allergens, phage wksl3 may be considered a virulent phage with no side effects. Analysis of genetic similarities between phage wksl3 and four of its relatives (SS3e, vB_SenS-Ent1, SE2, and SETP3) allowed wksl3 to be categorized as a SETP3-like phage. A single-dose test of oral toxicity with BALB/c mice resulted in no abnormal clinical observations. Moreover, phage application to chicken skin at 8°C resulted in an about 2.5-log reduction in the number of Salmonella bacteria during the test period. The strong, stable lytic activity, the significant reduction of the number of S. Enteritidis bacteria after application to food, and the lack of clinical symptoms of this phage suggest that wksl3 may be a useful agent for the protection of foods against S. Enteritidis and S. Typhimurium contamination.

Variable domain antibodies specific for viral hemorrhagic septicemia virus (VHSV) selected from a randomized IgNAR phage display library.

Phage display libraries are used to screen for nucleotide sequences that encode immunoglobulin variable (V) regions that are specific for a target antigen. We previously constructed an immunoglobulin new antigen receptor (IgNAR) phage display library. Here we used this library to obtain an IgNAR V region that is specific for viral hemorrhagic septicemia virus (VHSV). A phage clone (clone 653) was found to be specific for VHSV by the biopanning method. The V region of clone 653 was used to construct a 6 × His tagged recombinant IgNAR-653 V protein (rIgNAR-653) using the Escherichia coli pET system. The rIgNAR-653 protein bound specifically to VHSV, confirming its activity.

A Wireless, Mechanically Flexible, 25µm-Thick, 65,536-Channel Subdural Surface Recording and Stimulating Microelectrode Array with Integrated Antennas.

This paper presents a fully wireless microelectrode array (MEA) system-on-chip (SoC) with 65,536 electrodes for non-penetrative cortical recording and stimulation, featuring a total sensing area of 6.8mm×7.4mm with a 26.5µm×29µm electrode pitch. Sensing, data telemetry, and powering are monolithically integrated on a single chip, which is made mechanically flexible to conform to the surface of the brain by substrate removal to a total thickness of 25µm allowing it to be contained entirely in the subdural space under the skull.

Characterization and functional analysis of two PKR genes in fugu (Takifugu rubripes).

PKR (protein kinase R) is a serine-threonine kinase that inhibits protein synthesis by the phosphorylation of the eukaryotic translation initiation factor 2-alpha (eIF2α), and activates NFκB by inducing NFκB-inducing kinase and IκB (inhibitor of NFκB) kinase. This can lead to antiviral and anti-proliferative effects. In this study, the complete sequence and organization of two fugu PKR genes (fPKRs) were determined by in silico analysis and conventional PCR. The full-length fPKR1 and fPKR2 genes were 3832 bp and 4325 bp, which encoded 523 and 492 amino acids, respectively. Both encoded two dsRNA binding domains and a Serine/Threonine protein kinase domain, and showed very high similarity to green spotted puffer PKRs. Gene expression of the two fPKRs was measured by quantitative real-time PCR on tissue samples from healthy fish and peripheral blood leukocytes stimulated with polyinosinic:polycytidylic acid (PolyI:C) or lipopolysaccharides (LPS). The fPKRs were highly expressed in the skin and fPKR2 was significantly induced in PBLs by PolyI:C but not by LPS. The fPKRs inhibited translation of a luciferase reporter gene in a dose-dependent manner and induced transcriptional activity of a mammalian NFκB luciferase reporter. These results demonstrate that two PKRs in a single species can both be independently, but not equally, functional and support the hypothesis that fish PKRs have roles in the innate immune response similar to those of mammalian PKRs.

Evolutional conservation of molecular structure and antiviral function of a viral RNA receptor, LGP2, in Japanese flounder, Paralichthys olivaceus.

LGP2 is an important intracellular receptor that recognizes viral RNAs in innate immunity. To understand the mechanism of viral RNA recognition, we cloned an LGP2 cDNA and gene in Japanese flounder (Paralichthys olivaceus). Viral hemorrhagic septicemia virus-induced expressions of LGP2 mRNA were evaluated in vivo and in vitro by quantitative real-time PCR (Q-PCR) using primers based on the clone sequences. The expression of LGP2 mRNA in the kidney dramatically increased at 3 d postinfection. The expression of LGP2 mRNA also increased in the head kidney leukocytes stimulated with artificial dsRNA (polyinosin-polycytidylic acid) in vitro. To evaluate the antiviral activity of the flounder LGP2, three expression constructs containing pcDNA4-LGP2 (full-length), pcDNA4-LGP2ΔRD (regulatory domain deleted), and pcDNA4-Empty (as a negative control) were transfected into the hirame (flounder) natural embryo (hirame natural embryo) cell line. Forty-eight hours after transfection, the transfected cells were infected with ssRNA viruses, viral hemorrhagic septicemia virus, or hirame rhabdovirus. The cytopathic effects of the viruses were delayed by the overexpression of Japanese flounder LGP2. The Q-PCR demonstrated that mRNA expression levels of type I IFN and IFN-inducible genes (Mx and ISG15) in the hirame natural embryo cells overexpressing LGP2 were increased by polyinosin-polycytidylic acid and viral infections. These results suggest that Japanese flounder LGP2 plays an important role in the recognition of both viral ssRNA and dsRNA to induce the antiviral activity by the production of IFN-stimulated proteins.

Molecular characterization, expression and functional analysis of a nuclear oligomerization domain proteins subfamily C (NLRC) in Japanese flounder (Paralichthys olivaceus).

Pattern recognition receptors (PRRs) are involved in the effective innate defense against several microbes. Here, we identified a nucleotide-oligomerization domain (NOD)-like receptor subfamily C (NLRC) from Japanese flounder (Paralichthys olivaceus). Full-length transcript of JfNLRC is composed of 3976 bp encoding a protein of 1175 deduced amino acid residues. The presence of a signature nucleotide-binding domain (NACHT) and leucine-rich repeated domain (LRR) suggested that the protein is a member of the NLR family. Interestingly, its C-terminus presents an extra PRY/SPRY (B30.2) domain similar to fish in the Trim (finTrim) family. A phylogenic tree of JfNLRC revealed that full-length JfNLRC diverged from the NOD1 and NOD2 clusters, and the NACHT domain in JfNLRC was clustered within the NLRC3 group. Stimulation by formalin-killed Edwardsiella tarda, Streptococcus iniae, and lipopolysaccharide (LPS) showed that the JfNLRC expression was raised a few hours after stimulation, suggesting this novel protein is involved in the immediate response against both Gram-positive and Gram-negative bacteria. Furthermore, the IL-1ß mRNA expression level in JfNLRC-over-expressing HINAE cells was significantly increased, when compared to a control, after LPS-stimulation and E. tarda infection. These results suggested that JfNLRC probably induced IL-1ß gene expression mediated by LPS-stimulation.

Post-Synthesis Functionalization Enables Fine-Tuning the Molecular-Sieving Properties of Zeolites for Light Olefin/Paraffin Separations.

Zeolite molecular sieves are widely used in gas separation and shape-selective catalysis, but these applications often require discriminating differences as little as 0.1 Å. Molecular sieving with such size selectivity demands zeolites with highly tunable pore diameters and adsorption properties, which are technically challenging to prepare. Nevertheless, it is shown that a wide range of organic functional groups can be covalently functionalized onto the interior pore walls of the zeolites, MOR, LTL, FAU, and MFI, to systematically "tune" their effective pore diameters with respect to the size of organic groups. For organic functionalization, small and aggressive organic electrophiles are used (e.g., organo-halide and -diazonium) as grafting agents, which are accessible to the intracrystalline void space, forming a C-Ozeolite bond in a reaction with a bridging oxygen as proved by multiple analysis data. It is demonstrated that the post-functionalization can be used to tailor the molecular sieving action of a parent zeolite to give size-selective adsorbents for light olefin/paraffin separations. 4-Methoxybenzene-functionalized MOR separates ethylene from ethane with an ideal-adsorbed-solution-theory selectivity of ≈5873, whereas toluene-grafted MOR completely separates propylene/propane mixtures. Therefore, tailoring the molecular-sieving properties of zeolites by organic functionalization broadens their applications to challenging separations.

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

SUMMARY: WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions. AVAILABILITY: WEbcoli is freely accessible at http://webcoli.org. CONTACT: cheld@nus.edu.sg.

PESTAS: a web server for EST analysis and sequence mining.

SUMMARY: We have developed a web server for the high-throughput annotation of expressed sequence tags (ESTs) called pipeline for EST analysis service (PESTAS). PESTAS processes entire datasets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation. All annotated information is provided to the scientist and can be downloaded through a web browser. To get more relevant functional annotation results, a curation function was introduced with which biologists can easily change the best-hit annotation information. We included a gene chip module that detects gene expression differences between libraries by comparing accession number counts from BLAST search results. PESTAS also provides access to the pathway information of KEGG, which is useful for mapping the relationships among networks of annotated enzymes, and is especially valuable for those researchers interested in biological pathways. AVAILABILITY: PESTAS is available at http://pestas.kribb.re.kr/.

GarlicESTdb: an online database and mining tool for garlic EST sequences.

BACKGROUND: Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. DESCRIPTION: GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr. CONCLUSION: GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.

Antibiotic susceptibility and resistance of Streptococcus iniae and Streptococcus parauberis isolated from olive flounder (Paralichthys olivaceus).

The rates of antibiotic susceptibility and resistance were investigated in Streptococcus iniae and Streptococcus parauberis isolates obtained from diseased olive flounders (Paralichthys olivaceus) collected from fish farms in Jeju Island, Korea. Isolates of S. iniae (n=65) were susceptible to cefotaxime, erythromycin, ofloxacin, penicillin, tetracycline and vancomycin, as demonstrated by the minimum inhibitory concentration (MIC) test. Isolates of S. parauberis (n=86) were highly resistant to erythromycin (58% of the 86 isolates tested) and tetracycline (63% of the 86 isolates tested). Fifty-four isolates of tetracycline-resistant S. parauberis contained the tet(M/O/S) genes, of which 39 and 12 isolates contained the tet(M) and tet(S) genes, respectively, whereas 3 isolates contained both the tet(M) and tet(S) genes. Among the erythromycin-resistant isolates of S. parauberis (n=50) only 14 contained the erm(B) gene. These results suggest that the tet(S) and erm(B) genes of S. parauberis are involved in the acquisition of high-level resistance to erythromycin and tetracycline. Our findings reveal a high rate of antibiotic resistance among strains of S. parauberis and emphasize the need to develop an appropriate vaccine to reduce the use of antibiotics.

Synthesis of CuCl/Boehmite adsorbents that exhibit high CO selectivity in CO/CO2 separation.

We developed nanoporous adsorbent exhibiting unprecedented performance in separation of toxic carbon monoxide (CO). The adsorbent was prepared by dispersing CuCl on mesoporous boehmite via thermal monolayer dispersion route. A key point of the present synthesis is dispersing optimized amount of CuCl on the boehmite at a moderate temperature to maintain the characteristics of the boehmite. We performed a systematic study to reveal that a CuCl/boehmite composite (30wt% CuCl in total) thermally treated at 573K was the best optimized sample for CO separation. The CuCl/boehmite had a high capacity of CO adsorption (1.56mmolg-1) and an exceedingly low capacity of CO2 adsorption (0.13mmolg-1) under 100kPa of each gas at 293K. The CO/CO2 separation factor was 12.4. To the best of our knowledge, this value is the best on record. The achievement of this work is attributed to finding a new type of suitable supporting material: boehmite. The boehmite has a high affinity to CuCl, exhibits excellent dispersion of the CuCl, and achieves a superior CO adsorption capacity. However, it has a weak interaction with CO2. The CuCl/boehmite composite is a promising adsorbent for selective separation of CO from combustion exhaust and industrial off-gas streams.

Effects of Angelica gigas Nakai as an Anti-Inflammatory Agent in In Vitro and In Vivo Atopic Dermatitis Models.

We investigated the cellular and molecular mechanisms mediating the effects of Angelica gigas Nakai extract (AGNE) through the mitogen-activated protein kinases (MAPKs)/NF-κB pathway using in vitro and in vivo atopic dermatitis (AD) models. We examined the effects of AGNE on the expression of proinflammatory cytokines and chemokines in human mast cell line-1 (HMC-1) cells. Compound 48/80-induced pruritus and 2,4-dinitrochlorobenzene- (DNCB-) induced AD-like skin lesion mouse models were also used to investigate the antiallergic effects of AGNE. AGNE reduced histamine secretion, production of proinflammatory cytokines including interleukin- (IL-) 1ß, IL-4, IL-6, IL-8, and IL-10, and expression of cyclooxygenase- (COX-) 2 in HMC-1 cells. Scratching behavior and DNCB-induced AD-like skin lesions were also attenuated by AGNE administration through the reduction of serum IgE, histamine, tumor necrosis factor-α (TNF-α), IL-6 levels, and COX-2 expression in skin tissue from mouse models. Furthermore, these inhibitory effects were mediated by the blockade of the MAPKs and NF-κB pathway. The findings of this study proved that AGNE improves the scratching behavior and atopy symptoms and reduces the activity of various atopy-related mediators in HMC-1 cells and mice model. These results suggest the AGNE has a therapeutic potential in anti-AD.

Highly selective adsorption of CO over CO2 in a Cu(I)-chelated porous organic polymer.

Cu(I) species were successfully chelated to nitrogen atoms in a nitrogen-rich porous organic polymer (SNW-1) by mixing with a CuCl solution (Scheme 1). Although pristine SNW-1 adsorbs CO2 better than CO, Cu(I)-incorporated SNW-1 (nCu(I)@SNW-1) shows selective CO adsorption over CO2 because of the π-complexation of CO with Cu(I). To the best of our knowledge, this is the first CO/CO2 selectivity observed for POP-based materials. 1.3Cu(I)@SNW-1 exhibits high CO/CO2 selectivity (23) at 1bar and a large CO working capacity (0.6mmol/g) at 0.1-1bar. Moreover, the breakthrough and thermogravimetric experiments show that 1.3Cu(I)@SNW-1 can effectively separate CO from CO2 under dynamic mixture conditions and can be easily regenerated under mild regeneration conditions without heating the column. Furthermore, 1.3Cu(I)@SNW-1 exhibited a good stability under exposure to atmospheric air for 3h or 9h. These results suggest that chelating Cu(I) species to a nitrogen-rich porous organic polymer can be an efficient strategy to separate and recover CO from CO/CO2 mixtures.