Abstract: Disclosed is an enhanced method for rapid and cost-effective analysis of sequences of a microorganism by semi-conductor sequencing, preferably ion-torrent sequencing. This method provides for full length analysis and of multiple areas (e.g. genes) of multiple genomes. These methods identify genetic mutations of a particular gene that are responsible for conferring resistance or sensitivity to an antibiotic or other chemical compound. Multiple different species, strains and/or serotypes of a particular organism are rapidly and efficiently screened and mutations identified along with the complete genome of an organism. By selecting primers pairs of similar size and GC content that produce amplicons with sequences spanning the entire genome, a single PCR reaction analyzed by ion torrent methodology can determine the sequence of a complete genome. Methods are useful to sequences the genomes of viral agents, such as influenza virus, and bacterial agents, such as tuberculosis bacteria.

Abstract: The invention relates to a method for detection of a methicillin resistant coagulase positive Staphylococcus aureus (MRSA) strain by means of a sequence specific amplification reaction.

Abstract: Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the specific and differential detection of a non-Mycobacterium avium subsp. paratuberculosis (non-MAP) organism, wherein a non-MAP organism is a Mycobacterium avium complex (MAC) organism that does not belong to the Mycobacterium avium subsp. paratuberculosis (MAP) organism, from samples including veterinary samples, clinical samples, food samples, forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample. Exemplary non-MAP organisms including M. avium subsp. avium (MAA), M. avium subsp. hominissuis (MAH), and M. avium subsp. silvaticum (MAS) can be detected by the present compositions, kits and methods.

Abstract: Devices, systems, and methods for detecting molecules of interest within a collected sample are described herein. In certain embodiments, self-contained sample analysis systems are disclosed, which include a reusable reader component, a disposable cartridge component, and a disposable sample collection component. In some embodiments, the reader component communicates with a remote computing device for the digital transmission of test protocols and test results. In various disclosed embodiments, the systems, components, and methods are configured to identify the presence, absence, and/or quantity of particular nucleic acids, proteins, or other analytes of interest, for example, in order to test for the presence of one or more pathogens or contaminants in a sample.

Abstract: The disclosed invention include nucleic acid oligomers that may be used as amplification oligomers, including primers, as capture probes for sample preparation, and detection probes for detection of 16S rRNA from Atopobium vaginae in samples by using methods of specific nucleic acid amplification and detection.

Abstract: The present disclosure provides, inter alia, Thraustochytrium and relevant methods and reagents, including engineered regulatory sequences from and/or operative in Thraustochytrid or Thraustochytrium, selectable markers useful for engineering microorganisms such as Thraustochytrids, methods for mutagenizing microorganisms, novel strains produced by mutagenesis and methods and compositions related to production of particular compounds in microorganisms.

Abstract: Provided are methods for identification of plant glutamine synthetase inhibitors as well as the plant synthetase inhibitors identified. Further provided are methods of modulating glutamine synthetase activity in a plant, particularly weeds by applying to the plant or substrate for cultivating the plant a microorganism (e.g. Burkholderia strain) in an amount effective to modulate glutamine synthetase activity.

Abstract: The invention relates to isolated polypeptides that include amino acid sequences within botryococcene synthase from different algal species. In another aspect, the invention relates to a method for increasing the production level of a botryococcene hydrocarbon molecule in a cell. The method includes increasing expression of a polynucleotide sequence that encodes botryococcene synthase in the cell. In a further aspect, the invention relates to an algal cell having a polynucleotide sequence that is genetically engineered to express a higher level of botryococcene synthase than a corresponding wild type algal cell, wherein the cell produces an increased level of a botryococcene hydrocarbon molecule than a corresponding wild type algal cell.

Abstract: A method for screening biomolecules molecules is disclosed. One embodiment of the method includes inoculating an expression library or a portion of the expression library into an animal, monitoring the relative abundance of individual members of the expression library; and analyzing molecules expressed by members that show significantly reduced relative abundance after inoculation into the animal. Also disclosed is an expression vector and an expression library employing the vector.

Abstract: The invention relates to the polynucleotide sequence of a nontypeable strain of Haemophilus influenzae (NTHi) and polypeptides encoded by the polynucleotides and uses thereof. The invention also relates to NTHi genes which are upregulated during or in response to NTHi infection of the middle ear and/or the nasopharynx.

Abstract: The present disclosure relates generally to the field of nucleic acids and, more particularly, to aptamers capable of binding to toxins produced by Clostridium difficile; diagnostic kits and methods comprising such aptamers; and methods of making and using such aptamers.

Abstract: Provided herein are uses of genes for HOG, Ras and cAMP signal transduction pathways to treat fungal infection. To regulate the HOG pathway of Cryptococcus neoformans, roles of SSK1, TCO2, SSK2, PBS2, HOG1, ENA1 and NHA1 genes were investigated to find that a biosynthesis level of ergosterol is increased when these genes are inhibited. When the genes are inhibited, a large amount of ergosterol is distributed on a fungal cell membrane. Accordingly, since there are many working points of an ergosterol-binding antifungal agent, an efficiency of the ergosterol-binding antifungal agent can be considerably improved. To regulate the Ras and cAMP pathways of Cryptococcus neoformans, roles of RAS1, RAS2, CDC24, GPA1, CAC1, ACA1, PKA1, HSP12 and HSP122 genes were investigated to find that a sensitivity to a polyene- or azole-based drug is increased when these genes are inhibited.

Abstract: Devices and methods for preparing and assessing a liquid sample are described which include: a microfluidic microscopy device including an absorbent structure including at least one dry dye for a liquid and configured to convey a polar liquid from a first end of the absorbent structure through the at least one dry dye for a liquid to a second end of the absorbent structure, a support structure positioned adjacent to a first surface of the absorbent structure, a lid structure positioned adjacent to a second surface of the absorbent structure, and a clamping structure positioned to maintain a relative position of the support structure and the lid structure to form a tapered internal chamber adjacent to the second end of the absorbent structure.

Abstract: The present invention relates to a method for selectively enriching and/or isolating microbial and optionally additionally viral nucleic acids from samples that contain a mixture of microbial cells, freely circulating nucleic acids and higher eukaryotic cells, and optionally additionally viruses, in a liquid, and to a kit for selectively enriching and/or isolating intracellular and extracellular microbial nucleic acids, and optionally additionally viral nucleic acids, from samples that contain a mixture of microbial and higher eukaryotic cells, freely circulating nucleic acids, in particular extracellular microbial nucleic acids, and optionally additionally viruses in a liquid.

Abstract: A method of increasing biogenic production of a combustible gas from a subterranean geologic formation is described. The method may include extracting formation water from the geologic formation, where the extracted formation water includes at least a first species and a second species of microorganism. The method may also include analyzing the extracted formation water to identify the first species of microorganism that promotes the biogenic production of the combustible gas. An amendment may be introduced to the formation water to promote the growth of the first species of microorganism, and the biological characteristics of the formation water may be altered to decrease a population of the second species in the geologic formation.

Abstract: The present invention provides a molecular construct capable of fluorescent resonance energy transfer (FRET), comprising a linker peptide, and donor and acceptor fluorophore moieties, where the linker peptide is a substrate of a botulinum neurotoxin selected from the group consisting of synaptobrevin, syntaxin and SNAP-25, or a fragment thereof capable being cleaved by the botulinum neurotoxin, and separates the donor and acceptor fluorophores by a distance of not more than 10 nm, and where emission spectrum of the donor fluorophore moiety overlaps with the excitation spectrum of the acceptor fluorophore moiety; or where the emission spectra of the fluorophores are detectably different. Also provided are isolated nucleic acid expressing the construct, kits comprising said construct and cell lines comprising said nucleic acid. Further provided are methods of detecting a BoNT using the above described construct via FRET, and methods for detecting a BoNT using surface plasmon resonance imaging.

Abstract: The present invention provides nucleic acid aptamers that bind to Plasmodium proteins lactate dehydrogenase and histidine-rich protein II, and uses thereof for the diagnosis of malaria. Aptamers against histidine-rich protein II may be used to detect the presence of Plasmodium species in general, whereas aptamers against lactate dehydrogenase can be used to specifically detect Plasmodium falciparum.

Abstract: The method for isolating nucleic acids from a food sample comprising the following steps: a) obtaining a food enrichment culture; b) transferring a portion of the food enrichment culture into a reaction vessel thereby providing a food enrichment sample and providing a water-immiscible phase in contact with the food enrichment culture; c) lysing the food enrichment sample to provide a lysed sample; d) isolating nucleic acids from the lysed sample. Food enrichment culture samples are known to contain high concentrations of organic and/or liposoluble inhibitors. By contacting the enrichment culture sample with a water-immiscible phase before the actual DNA extraction procedure starts, part of the lipophilic inhibitors is expected to cross the phase interface due to an enhanced solubility in the organic phase and thereby become depleted.

Abstract: Methods for the detection and typing of bacterial strains from food products and dietary supplements, environmental samples, in vivo/in vitro samples, and for studying the natural diversity of the species are disclosed. Potential applications also include product development and/or detection and differentiation of new bacterial strains.

Abstract: A nucleic acid aptamer comprising the nucleotide sequence shown herein as SEQ ID No. 5, 6, 7, 8, 9, 10, 1, 2, 3 or 4 or a fragment thereof or a sequence which is at least 80% identical therewith and use of nucleic aptamers to detect the presence of pathogenic bacteria in a sample, particularly in a complex matrix—such as a food system.

Abstract: Disclosed herein is a method of detecting and identifying antigens that are shed into human bodily fluids during infection. The disclosed method allows circulating antigens associated with a particular infection to be detected within minutes or hours from testing as compared to days required with the current methods. Methods of identifying diagnostic indicators/targets for a given condition or disease are disclosed which include immunizing a veterinary subject with biological fluids obtained from a human infected with particular antigens to identify diagnostic targets for immunoassay. Also disclosed are methods of diagnosing and monitoring a B. pseudomallei-associated condition, such as melioidosis. Point-of-care immunoassays are also provided that can be used to diagnose or monitor the efficacy of a B. pseudomallei-associated condition treatment. These immunoassays can also be used for rapid diagnosis of infection produced by B. pseudomallei, such as meliodosis.

Abstract: The present invention provides a method of detecting dermatophyte, which does not require a complicated operation such as an enzyme treatment and a heat treatment. The present invention provides a method of detecting dermatophyte, including a step of extracting a dermatophyte component from a sample with a treatment liquid containing a non-ionic surfactant or a zwitterionic surfactant, and a kit for diagnosing dermatophyte infection, containing a treatment liquid comprising the above surfactant, and an antibody specifically recognizing a dermatophyte component, which are housed in separate containers.

Abstract: The invention relates to a method for detecting the presence or absence of a bacterial pathogen in a biological sample obtained from a human or animal subject, using an internal control. In particular, the invention relates to a method for detecting the presence or absence of Streptococcus equi in an equine sample using a control bacterial strain as internal control for DNA extraction and PCR. The invention also relates to host cells (such as bacterial cells) and nucleic acids for use as internal standard in said method in addition to diagnostic kits comprising said host cells and nucleic acids.

Abstract: Provided herein are vaccine vectors including an antigenic polypeptide and an HMGB1 polypeptide present on the surface of the vaccine vector. Compositions comprising the vaccine vectors are also provided and include a pharmaceutically acceptable carrier, suitably a carrier for oral or nasal administration. Also provided are methods of enhancing immune responses, in particular antibody immune response and suitably an IgA response, by administering the vaccine vectors or compositions disclosed herein to a subject.

Abstract: The invention relates to a method of identifying an Aspergillus terreus or an Aspergillus niger fungal species in patient tissue or body fluid and to primers and probes for use in such a method.

Abstract: The present invention relates to probiotic compositions and methods of using such compositions. In particular, the present invention provides method of using Faecalibacterium spp. to improve weight gain, provide prophylaxis against diarrhea and/or improve feed efficiency in an animal.

Abstract: The present invention provides assays and methods for efficiently testing a polynucleotide of interest for a phenotype in a root. In some embodiments, the assays and methods include regenerating green tissue that is transgenic for at least one polynucleotide of interest into one or more transgenic plantlets that have at least one transgenic root. Further provided are methods of making a root assay by contacting green tissue with a first rooting medium to produce a plantlet and a plurality of roots. Additionally provided are methods of assaying for insecticidal activity on a live root. Accordingly provided herein is a substantially contamination-free, root bioassay. Further provided are methods of identifying a promoter having activity in a root.

Abstract: Disclosed herein, inter alia, is method, kit and systems for detecting a pathogen infection in a bodily sample, the method comprising (i) staining said bodily sample with two or more dyes, comprising at least one dye predominantly staining DNA to thereby provide differential staining between DNA and at least one other cellular component being different from DNA; (ii) identifying at least a first stained area comprising the DNA, if exists in the sample, and at least one other stained area comprising the other cellular component; (iii) extracting structural features for the first stained area and the at least one other stained area, said structural features comprise at least one of (i) size of at least one of the first stained area and one other stained area and (ii) location of said first stained area and said at least one other stained area one with respect to the other; and (iv) determining the presence of a suspected pathogen in the bodily sample if a first stained area was identified and said structural fe

Abstract: Use of the ssrA gene or tmRNA, an RNA transcript of the ssrA gene, or fragments thereof as target regions in a nucleic acid probe assay for the detection and identification of prokaryotic and/or eukaryotic organisms is described. Nucleotide sequence alignment of tmRNA sequences from various organisms can be used to identify regions of homology and non-homology within the sequences which in turn can be used to design both genus specific and species specific oligonucleotide probes. These newly identified regions of homology and non-homology provide the basis of identifying and detecting organisms at the molecular level. Oligonucleotide probes identified in this way can be used to detect tmRNA in samples thereby giving an indication of the viability of non-viral organisms present in various sample types.

Abstract: The present invention relates to a kit for detection of association of a peripheral cellular membrane binding protein with cellular membranes in living cells and methods thereof. The kit includes a first nucleic acid construct comprising a first nucleic acid molecule encoding a first fusion protein comprising a peripheral cellular membrane binding protein or membrane binding domain thereof operatively coupled to DNA binding and transactivation domains of a naturally occurring or chimeric transcription factor and a first promoter operatively associated with the first nucleic acid molecule. A second nucleic acid construct comprises a second nucleic acid molecule encoding a reporter protein and a second promoter responsive to the DNA binding and transactivation domains of the first fusion protein. The second promoter is operatively associated with the second nucleic acid molecule. Activation of the second promoter results in expression of the reporter protein. Also disclosed is a transgenic non-human animal.

Abstract: The present invention relates to a method for the specific detection and/or identification of Staphylococcus species, in particular Staphylococcus aureus, using new nucleic acid sequences derived from the ITS (Internal Transcribed Spacer) region. The present invention relates also to said new nucleic acid sequences derived from the ITS region, between the 16S and 23S ribosomal ribonucleic acid (rRNA) or rRNA genes, to be used for the specific detection and/or identification of Staphylococcus species, in particular of S. aureus, in a biological sample. It relates also to nucleic acid primers to be used for the amplification of said spacer region of Staphylococcus species in a sample.

Abstract: A method of evaluating inhibitory effect on damp-dry malodor, containing the steps of: bringing microorganisms which produce damp-dry malodor-causing substances and a test substance into contact with each other in the presence of a sebaceous dirt component; detecting expression of at least one kind of gene selected from a fatty acid desaturase gene and a ? oxidation-related enzyme gene derived from the microorganisms; and thereby evaluating a damp-dry malodor inhibitory function of the test substance based on a change in expression amount of the at least one kind of gene.

Abstract: A highly sensitive method of analyzing a sample for the presence or activity of botulinum neurotoxin (BoNT) or antibodies specific for botulinum neurotoxin is disclosed. In one embodiment, the method comprises the steps of preparing primary non-human mammalian or avian spinal cord cells, and exposing the cells to a test sample, in parallel with a control sample, and examining the extent of cleavage of the intracellular neuronal target protein in both the test and control sample.

Abstract: Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted by that enzyme.

Abstract: The present invention relates to host cells having modified lipid-linked oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar transporters and mannosidases to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified lipid-linked oligosaccharides are created or selected. N-glycans made in the engineered host cells have a GlcNAcMan3GlcNAc2 core structure which may then be modified further by heterologous expression of one or more enzymes, e.g., glycosyl-transferases, sugar transporters and mannosidases, to yield human-like glycoproteins. For the production of therapeutic proteins, this method may be adapted to engineer cell lines in which any desired glycosylation structure may be obtained.

Abstract: The present invention relates to a three-dimensional structure of a complex explored by crystallization of the complex of NanR which is a key pathogenic regulatory protein of Vibrio vulnificus and ManNA6P which is a NanR regulator. Further, the present invention relates to a modified NanR protein, a polynucleotide encoding the protein, a vector including the polynucleotide, and a transformant including the vector. Furthermore, the present invention relates to a method for screening a substance regulating interaction between NanR and the transcriptional control region of nan operon which is a gene cluster regulated by NanR, or a substance regulating interaction between NanR and ManNAc-6P, by designing three-dimensional structure of the complex, and to an antibacterial composition including the screened substance.

Abstract: The present invention provides compositions, methods and kits for the species-specific detection of Pseudomonas aeruginosa.

Abstract: The present disclosure provides methods to detect pests in liquid culture systems for the growth of microalgae. The disclosure further provides methods to treat and control pests in a liquid system and for methods to increase yields of microalgae grown in a liquid culture systems. Methods are provided for the growth, monitoring, treatment and harvesting of microalgae from liquid culture systems.

Abstract: The invention comprises an oligonucleotide selected from the group comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3; SEQ ID NO: 4; SEQ ID NO: 5 and SEQ ID NO: 6. The invention also comprises a complementary oligonucleotide of the oligonucleotide selected from the group comprising SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3; SEQ ID NO: 4; SEQ ID NO: 5 and SEQ ID NO: 6, an oligonucleotide being at least 80% homologous thereto, a truncated portion of any of the aforementioned, or a pairing of any of the aforementioned.

Abstract: Particular aspects provide a method of sampling, testing and validating test lots (e.g., single-unit production lots), comprising: assembling a plurality of product portions from each of a plurality of test lots and combining the collected product portions to provide a corresponding set of test lot samples (wherein each test lot sample is attributed to a particular corresponding test lot); enriching the set of test lot samples; removing equal portions of each enriched sample, and combining the removed portions to provide a modular composite sample; and testing of the modular composite sample for the target agent/organism, wherein where such testing is positive, individual test lots may nonetheless yet be validated by further testing of a respective enriched test lot sample and obtaining a negative test result. The methods have broad utility for monitoring all sorts of test lots (e.g., environmental lots, production lots, pharmaceutical lots, etc.

Abstract: The invention relates generally to compositions and methods for disrupting cells (e.g., disrupting cellular and nuclear membranes). In particular, the invention provides modified solid surfaces (e.g., bead surfaces) and their use in disruption of cellular membranes (e.g., during cellular lysis procedures (e.g., for recovery of nucleic acid (e.g., DNA or RNA) from mechanical cell lysis)). Compositions and methods of the invention find use in a wide range of applications including molecular biology and medical science.

Abstract: Mycobacterium bovis BCG is a potent stimulator of the cellular immune response and has potential as a recombinant vaccine vector. Disclosed are BCG strains that generate greater MHC class I presentation of a transgenic protein, relative to the unmutated parental strain, and that improve a recipient's CD8+ T cell response against the transgenic protein following vaccination. The mycobacterial constructs and their respective t/ansposon mutant BCG strains exhibit increased immunogenicity that is several times greater than responses generated by the parental strain and other existing modified rBCG strains. Furthermore, upon introducing the SIV gag gene into these novel strains, we observed that these strains primed for increased CD8+ T cell responses in a heterologous prime/boost regimen, comparable to levels generated by plasmid DNA vaccines. Creation of a second generation rBCG vector that may be utilized as a vaccine vector for immunizing against a variety of pathogens.

Abstract: The invention relates to methods and reagents for determining efficacy of vaccine, particularly of a tuberculosis vaccine.

Abstract: Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

Abstract: Methods of identifying genes conferring ethanol tolerance in yeasts, genes that confer ethanol tolerance, and mutant strains used to identify such genes are described. A gene herein designated HpETT1 was isolated from the yeast Hansenula polymorpha. Expression of HpETT1 in an ethanol sensitive mutant H. polymorpha strain designated 7E complimented ethanol sensitivity of the mutant. When multiple copies of the HpETT1 were integrated into the genome and overexpressed, the transformed strain demonstrated approximately 10-fold greater resistance to ethanol and resistance to the protein misfolding agent AZC. Expression of HpETT1 also increased ethanol tolerance in Saccharomyces cerevisiae. HpEtt1 has 39% sequence identity to a previously identified protein from S. cerevisiae denoted MPE1, however, the MPE1 gene does not confer ethanol resistance to the 7E mutant.

Abstract: Disclosed are compositions, kits, and methods for detecting, extracting, visualizing, characterizing, and/or identifying one or more protozoa. Various types of polymerase chain reaction techniques in connection with specifically designed oligonucleotide probes can be used to detect a variety of, e.g., pathogenic, protozoa in samples.

Abstract: A respirable composition for treatment of a bacterial infection includes one or more active bacteriophages in combination with a pharmaceutically acceptable respirable carrier. The composition includes a carbohydrate carrier, and is prepared as fine powder. In another aspect, bacteriophages are provided in a liquid carrier for administration by nebulization. In one aspect, the bacteriophages have anti-bacterial activity against one or more species or strains of Burkholderia cepacia complex (BCC) bacteria. The invention further relates to the use of a BCC bacteriophage to treat a BCC infection, in particular in an individual suffering from cystic fibrosis.

Abstract: A method for enrichment and isolation of microbial cells and microbial nucleic acids from a biological sample is described. The method comprises (i) adding to an initial volume of biological sample a differential cell lysis solution to obtain a final concentration of 0.1 to 1% of SDS in the sample; (ii) mixing the solution obtained in step (i) for a period of time sufficient to lyse the host cells present in the biological sample, while preserving the integrity of cells; and (iii) separating the microbial cells from the lysed host cells components. Differential cell lysis solutions and kits for practicing the method of the present invention are also provided.

Abstract: By designing a retrogression-progression model in combination with oral microbial community analysis, the present invention provides a method of identifying a biomarker indicative of a subject mammal's condition, wherein the condition is selected from presence of the first disease, severity of the first disease, sensitivity to the first disease, and combinations thereof. The present invention further provides a computer-aided system of identifying a biomarker indicative of a subject mammal's condition.

Abstract: This invention features systems and methods for the detection of analytes, and their use in the treatment and diagnosis of disease.