Abstract: Biomarkers can be assessed for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, or the stage or progression of a disease. Circulating biomarkers can be detected and optionally used in profiling of physiological states or determining phenotypes. These include nucleic acids, protein, and circulating structures such as vesicles. Biomarkers can be assessed for diagnostic, prognostic or theranostic purposes, e.g., to select candidate treatment regimens for diseases, conditions, disease stages, and stages of a condition, and can also be used to determine treatment efficacy. Examples of useful circulating biomarkers include polypeptides, nucleic acids (e.g., DNA, mRNA, microRNA) and vesicles.

Abstract: A full process control for use with a molecular assay and a method of determine the efficacy of the molecular assay. A full process control can include a fixed cell, and specifically can include a fixed vegetative cell. A method of determining the efficacy of a molecular assay can include providing an internal control, mixing the internal control with a sample, lysing the internal control and the sample, and detecting the lysis product. The full process control and/or the internal control can be Bacillus subtilis cells.

Abstract: The present invention provides compositions and methods for detecting Candidatus Liberibacter infection and Huanglongbing disease in a citrus plant by detecting the expression of small RNAs such as miRNA and siRNA. The invention also provides methods for treating Huanglongbing disease in a citrus plant by contacting the plant with a phosphorus containing solution.

Abstract: The invention relates to a polypeptide, a corresponding nucleic acid molecule, a construct and/or vector and/or cell comprising such nucleic acid molecule and/or a composition comprising said polypeptide, nucleic acid molecule, construct, vector and/or cell. The invention further relates to such composition for medical use, preferably for use in treating an infectious disease. Furthermore, the invention relates to the use of said polypeptide, nucleic acid molecule, construct, vector, cell and/or composition as an antimicrobial, preferably as a food additive or disinfectant, or for detecting bacteria, preferably in a diagnostic application.

Abstract: The invention relates to the field of combating leishmaniases. Said invention results from the isolation, from wild isolates of Leishmania major, of a protein-coding gene known as LmPDI which has two regions that are identical to the sequence (Cys-Gly-His-Cys) of the potential active site of the protein disulphide isomerase (PDI). The LmPDI protein is predominantly expressed in the most virulent isolates of the parasite. Said protein forms a novel therapeutic target for developing anti-leishmaniasis medicaments and a novel element that can be used in the composition of immunogenic, and possibly vaccinating, preparations which are intended to protect a human or animal host against Leishmania.

Abstract: The invention provides variants of the Thermoanaerobacter brockii CglT beta-glucosidase that have improve beta-glucosidase activity compared to the wild type enzyme. The invention also provides polynucleotides that encode the variants, as well as methods of producing the variants, enzyme compositions comprising the variants, and methods for using the variants in industrial applications.

Abstract: The present invention provides a standardized method and a kit for an accurate quantification of HAV in clinical and food samples. The general approach is based on the use of several controls to measure the efficiency of those critical steps of the quantification: the nucleic acids extraction and the RT-PCR reactions. The kit comprises: a Mengo virus mutant strain with the same growth properties than those of the wild-type Mengo virus and with no pathogenic capacity; a single stranded RNA molecule corresponding to a fragment of the HAV genome; primers that specifically bind to regions of the 5? non coding region of the HAV genome; a detectable labeled probe that specifically binds to the amplimer resulting from the RT-PCR; and an appropriate molecule to generate an standard curve for the quantification of HAV.

Abstract: An object of the present invention is to provide a method for producing ethanol from polysaccharide alginate contained in a large amounts in brown algae, using the alginate assimilation capacity of the Sphingomonas sp. strain A1 and the strong ethanol production capacity of bacteria such as Zymomonas mobilis. Specifically, a method for producing ethanol using alginate as a raw material comprises causing genes encoding proteins and enzymes involved in Sphingomonas sp. strain A1-derived alginate assimilation and genes encoding enzymes involved in ethanol production to co-exist in a single microorganism and then culturing the microorganism in a medium containing alginate.

Abstract: TRFs useful for identifying strains of interest are provided. A method of identifying one or more strain that can be used as a direct-fed microbial is also provided. One or more strain identified by the method is additionally provided. A method is also provided for administering to an animal an effective amount of the one or more strain. Additionally provided is an isolated strain chosen from at least one of Lactobacillus acidophilus strain P1B c6 (NRRL B-50103), Lactobacillus salivarius strain o246e 33w (NRRL B-50102), Pediococcus acidilactici strain o246e 42 (NRRL B-50171), and Pediococcus acidilactici strain P1J e3 (NRRL B-50101). An isolated strain having all of the identifying characteristics of one of the strains listed above is also provided. One or more strain can be administered as a direct-fed microbial to an animal. Methods of preparing a direct-fed microbial are also provided.

Abstract: The invention relates to an in vitro method for the detection of bacteria of the Salmonella spp. genus by means of a quantitative polymerase chain reaction using specific primers for the pathogen from DNA and RNA samples from the microorganism. The method is useful in the detection of viable and non-viable microorganisms of Salmonella spp. in environmental, clinical and food samples. Likewise, the invention also relates to a kit used for putting the method into practice.

Abstract: A process of pathogen identification and a transport container are disclosed. The process includes positioning a porous material containing a sample into an receptacle of a transport container, facilitating transport of the transport container through a mail or parcel service, removing the porous material, the receptacle of the transport container, collecting the sample from the porous material, analyzing the preserved nucleic acid, or a combination thereof. The porous material degrades the sample and preserves nucleic acid. The analyzing identifies a plurality of sequences within the preserved nucleic acid in a parallel manner.

Abstract: The present invention relates to a method for in vivo detection of a biofilm infection residing in a mammal, the method comprising (i) administering to the mammal a diagnostic-effective amount of a biofilm-specific probe, wherein the probe comprises a bio film-targeting moiety and a paramagnetic nanoparticle core; and (ii) imaging the mammal to detect the presence of the biofilm infection by observing the mammal using a magnetic resonance diagnostic technique after the biofilm-specific probe has been provided sufficient time to selectively bind to the bio film infection that may be present in the mammal. The invention also relates to methods of treatment of a bio film infection, and compositions and kits useful in the detection and/or treatment of bio film infections.

Abstract: The present invention provides a method for the transfection of filamentous fungal cells, comprising providing a multitude of containers, filling into each container an amount of polymer needed for the transfection, filling the cells to be transfected as well as an aqueous solution of transfection reagent into each of the containers, incubating the resulting mixture, removing the transfection reagent from the incubated mixture; and selecting the cells which have been transformed, characterized in that the total volume of the incubating mixture is less than 1 ml per container. Furthermore, the present invention provides the use of transformed filamentous fungal cells for the production of proteins or metabolites.

Abstract: Methods of the invention generally involve using magnetic particles to isolate low levels of pathogens from a samples and identifying genes expressed by those pathogen. In one aspect, the method includes obtaining a sample comprising a pathogen, forming magnetic particle/target complexes, separating the magnetic particle/target complexes using magnetic fields, and determining an expression profile of a nucleic acid derived from the target.

Abstract: The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes methods for assaying a location to determine the amount of pest infestation, or assaying a plant for its ability to resist infection, and using this information to make agronomic treatment and/or breeding decisions. The invention also provides methods for breeding cotton plants containing one or more quantitative trait loci that are associated with resistance to reniform nematode infection. The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring reniform resistance as a source of reniform resistant alleles for introgression into elite germplasm in a breeding program, thus producing novel elite germplasm comprising one or more reniform resistance loci.

Abstract: A detection apparatus and method for the automatic detection of particles, in particular biological particles, in a sample. The detection apparatus comprises a detection device for recording the particles, and a fluidic device for automatically conveying the sample to the detection device. The fluidic device comprises a treatment device for the automatic treatment of the particles for the purpose of detection, and the detection device comprises a flow cytometer for recording at least one physical parameter of the treated particles. The detection method includes operations performed by the detection device, the fluidic device, the treatment device and the flow cytometer.

Abstract: A method for detecting inflammation in the urinary tract or urethra of a patient, especially urethritis, comprises a) contacting leucocytes obtained from a urine sample provided by the patient with a luminescence reagent which emits light on reaction with an oxidant; b) adding an activator to the mixture of leucocytes and luminescence reagent; c) continuously monitoring and/or measuring light emitted by the luminescence reagent over a predetermined time period commencing before and ending after the addition of the activator. The light emission is indicative of the presence or absence of inflammation in the urinary tract or urethra of the patient. The urine sample is preferably a sample of first pass urine. The method makes possible a diagnosis especially of urethritis and, in particular, urethral infections selected from Chlamydia trachomatis and Neisseria gonorrhoeae, which can be carried out quickly without invasive procedures.

Abstract: A real-time method employing a portable peptide-containing potentiometric biosensor, can directly detect and/or quantify bacterial spores. Two peptides for specific recognition of B. subtilis and B. anthracis Sterne may be immobilized by a polysiloxane monolayer immobilization (PMI) technique. The sensors translate the biological recognition event into a potential change by detecting, for example, B. subtilis spores in a concentration range of 0.08-7.3×104 CFU/ml. The sensing method exhibited highly selective recognition properties towards Bacillus subtilis spores over other kinds of spores. The selectivity coefficients of the sensors for other kinds of spores are in the range of 0-1.0×10?5. The biosensor method not only has the specificity to distinguish Bacillus subtilis spores in a mixture of B. subtilis and B. thuringiensis (thur.) Kurstaki spores, but also can discriminate between live and dead B. subtilis spores. Furthermore, the sensing method can distinguish a Bacillus subtilis 1A700 from other B.

Abstract: A molecular net formed as a branched pseudorandom copolymer including two broad classes of subunits: capture agents and linking agents. The subunits self-assemble to form a structure capable of binding to predetermined targets. The binding can then be detected.

Abstract: The present disclosure relates, according to some embodiments, to a method of stabilizing a molecule (e.g., a biomolecule) in a bodily fluid comprising: (1) providing a stabilizing solution comprising: (a) an amount of a divalent metal chelator selected from the group consisting of ethylenediaminetetraacetic acid (EDTA), (ethylenebis(oxyethylenenitrilo))tetraacetic acid (EGTA), and 1,2-bis(2-aminophenoxy)ethane-N,N,N?,N?-tetraacetic acid (BAPTA) and salts thereof in the range of from about 0.001 M to about 2 M; and (b) an amount of at least one chelator enhancing component selected from the group consisting of lithium chloride, guanidinium chloride, guanidinium thiocyanate, sodium salicylate, sodium perchlorate, and sodium thiocyanate in the range of from about 0.1 M to about 10 M; and (2) adding the stabilizing solution to the bodily fluid, thus stabilizing the molecule.

Abstract: Contemplated methods and devices comprise detecting the presence of a pathogen in a biological host. In certain implementations, a sample is provided from a biological host. A biosensor is provided, the biosensor having a first probe configured to detect a control marker in the sample, the control marker being an endogenous element of the biological host. The biosensor has a second probe configured to detect the presence of a target marker in the sample, the target marker being from a pathogen in the biological host. The sample is applied to the biosensor, and the presence or absence of the control marker in the sample is identified using the first probe. The presence or absence of the target marker in the sample is identified using the second probe.

Abstract: One major problem in diagnosis methods presently available for anthrax is that these methods require several days to produce a result. The only existing treatment for anthrax requires administration soon after infection at a time when patients are exhibiting only mild flu-like symptoms. Thus, a patient may be days beyond the time when treatment would be effective by the time a diagnosis is made. The present invention reduces diagnosis time to as little as four hours providing same day identification of anthrax radically increasing the odds of delivering proper treatment and patient recovery. The rapid identification of anthrax lethal factor activity exhibited by the instant invention is also amenable to in vivo screening protocols for the discovery and development of anthrax vaccines and lethal factor inhibitors. The instant invention isolates and concentrates lethal factor and lethal toxin from nearly any biological sample.

Abstract: A method of culturing fastidious bacteria where a conditioned cell culture medium is prepared in which eukaryotic cells have been cultured, but where the medium is substantially free of the cultured cells. Fastidious bacteria are cultured in the medium. The conditioned cell culture medium can contain secreted factors from the cells. These factors promote the growth of the fastidious bacteria. The fastidious bacterial culture is maintained for a time period sufficient for the fastidious bacteria to multiply. The fastidious bacteria are analyzed using PCR, DNA sequencing or microbiology characterization.

Abstract: Described herein are methods of detecting a wound infection and for detecting the presence or absence of microorganisms, for example, wound pathogens in a sample, by contacting a sample with an enzyme produced and/or secreted by the bacteria, and detecting modification or the absence of modification of the substrate, as an indicator of the presence or absence of the enzyme in the sample. The present invention also features a biosensor for detecting the presence or absence of bacteria in a sample.

Abstract: Disclosed are compositions and methods for isolating, detecting, amplifying, and quantitating Mycobacterium-specific nucleic acids in a sample. Also disclosed are compositions and diagnostic kits comprising Mycobacterium IS6110-specific oligonucleotide amplification primers and labeled oligonucleotide detection probes that specifically bind to the amplification products obtained therefrom. Also disclosed are compositions and methods for the isolation and characterization of nucleic acids that are specific to one or more tubercular pathogens, including Mycobacterium tuberculosis, in particular, from a wide variety of samples including those of biological, environmental, clinical and/or veterinary origin.

Abstract: Provided are a single-stranded nucleic acid aptamer specifically binding to E. coli and a method for detecting E. coli using the same. The method, kits or sensors of the present disclosure enable E. coli to be specifically detected among microorganisms existing in a water system, but also be applied in fields such as food sanitation or medical diagnosis.

Abstract: Compositions and methods are provided that relate to the bioremediation of chlorinated ethenes, particularly the bioremediation of vinyl chloride by Dehalococcoides-like organisms. An isolated strain of bacteria, Dehalococcoides sp. strain VS, that metabolizes vinyl chloride is provided; the genetic sequence of the enzyme responsible for vinyl chloride dehalogenation; methods of assessing the capability of endogenous organisms at an environmental site to metabolize vinyl chloride; and a method of using the strains of the invention for bioremediation.

Abstract: Methods of diagnosing Clostridium difficile infection and compounds used in the methods are provided. The diagnostic methods are specific and sensitive methods for detecting a host cell response and, in some aspects, a target response, i.e. a Clostridium difficile toxin, in an individual infected with Clostridium difficile. The methods comprise detecting in a stool specimen or fluid exposed to the stool specimen a Clostridium difficile toxin, or a fragment thereof, and an increase in a colonic epithelial cell protein exemplified by a non-muscle tropomyosin. Also provided are kits comprising reagents for detecting host cell proteins and Clostridium difficile toxins.

Abstract: Methods and materials are disclosed relating to an improved method for amplifying a signal in a diagnostic assay for a nucleic acid, comprising the steps of providing an amplification polymer bound to a nucleic acid analyte, wherein the amplification polymer comprises a plurality of amine groups; binding amine groups on the amplification polymer with a detectable label complex; and reacting under high salt conditions an acetylating compound with amine groups not bound with a detectable label complex.

Abstract: The invention provides nucleic acids, collections of nucleic acids, assay kits, and methods for the sensitive and specific detection of microorganisms in a foodstuff. The nucleic acid consists of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-45.

Abstract: The present invention relates to compositions and methods for the use of enzymes composed of nucleic acid and/or protein enzymes to generate and amplify a signal indicative of the presence of a target. More particularly, the invention relates to compositions comprising nucleic acid structures that serve as partial or complete enzyme substrates and methods for using these structures to facilitate detection of targets.

Abstract: The invention relates to a method of identifying a specific fungal species in patient tissue or body fluid. The method comprises the steps of extracting and recovering DNA of the fungal species from the patient tissue or body fluid, amplifying the DNA, hybridizing a probe to the DNA to specifically identify the fungal species, and specifically identifying the fungal species. The invention also relates to a method of identifying a mycotoxin in patient tissue or body fluid. The method comprises the steps of extracting and recovering the mycotoxin from the patient tissue or body fluid, contacting the mycotoxin with an antibody directed against the mycotoxin, and identifying the myocotoxin. Both of these methods can be used to determine if a patient is at risk for or has developed a disease state related to a fungal infection, and to develop an effective treatment regimen for the patient.

Abstract: Disclosed are compositions for isolating populations of nucleic acids from biological, forensic, and environmental samples. Also disclosed are methods for using these compositions as one-step formulations for killing pathogens, inactivating nucleases, and releasing polynucleotides from other cellular components within the sample, and stabilizing the nucleic acids prior to further processing or assay. The disclosed compositions safely facilitate rapid sample collection, and provide extended storage and transport of the samples at ambient or elevated temperature without contamination of the sample or degradation of the nucleic acids contained therein. This process particularly facilitates the collection of specimens from remote locations, and under conditions previously considered hostile for preserving the integrity of nucleic acids released from lysed biological samples without the need of refrigeration or freezing prior to molecular analysis.

Abstract: Compositions, methods and kits are provided for identifying at least one virulence factor of a Gram-negative bacterial strain, and for preparing attenuated bacterial strain vaccines or a modulator that selectively binds to or inhibits expression of the virulence factor. The Gram-negative bacterial strain is a short facultatively aerobic or micro-aerobic rod or an enteric strain including at least one pathogen selected from the group of: Salmonella, Escherichia, Yersinia, Klebsiella, Shigella, Enterobacter, Serratia, Pseudomonas, and Citrobacter. Novel genes encoding virulence factors are identified, so that non-virulent mutant strains are available for vaccine development.

Abstract: A diagnosis kit is configured to detect whether or not an extraneous organism exists in a red blood cell by using a biological specimen containing the red blood cell, and a stain solution capable of staining nucleic acid. The kit includes at least one diagnosis plate. The diagnosis plate includes a first chamber configured to store the stain solution and to have the biological specimen injected into the stain solution, a channel connected to the first chamber, and a test plate connected to the channel. A second chamber is connected with the test plate. The channel is configured to extract the red blood cell. The second chamber can collect a part of the biological specimen and a part of the stain solution. This diagnosis kit can detect extraneous organisms in the red blood cells easily with a small amount of the biological specimen.

Abstract: The present invention is a method of extracting infectious pathogens from a volume of blood including the steps of creating a fibrin aggregate confining the pathogens and introducing a fibrin lysis reagent to expose the pathogens for analysis. The fibrin lysis reagent is preferably composed of plasminogen and streptokinase frozen in coincident relation until the fibrin lysis reagent is needed whereby streptokinase enzymatically reacts with plasminogen to form plasmin upon thawing. The plasminogen is suspended in an aqueous salt solution prior to freezing including NaCl and Na3PO4.

Abstract: Methods, pharmaceutical compositions, and kits are provided which includes accurately sampling a RNA from a tissue of an animal and analyzing RNA in the tissue of the animal as an indicator of physiological state, infectious disease, neoplastic disease, autoimmune disease, inflammatory disease, cardiovascular disease, atherosclerotic disease, or neurological disease in the animal. A method is provided which includes administering at least one compound to an animal wherein the at least one compound is configured to prevent the cleavage of at least one tissue RNA by a ribonuclease. The method further includes collecting a sample of at least a portion of tissue from the animal.

Abstract: The invention relates to a process involving analyzing the presence of arsenic in a sample, comprising the following steps: (a) contacting a sample suspected of containing arsenic on a solid support functionalized with a DNA fragment comprising an ArsR protein binding site, site on which an ArsR protein is attached, the presence arsenic causing separation of the ArsR protein from the DNA fragment; (b) incubation of the sample in contact with the said support; (c) elimination of ArsR protein separated from the DNA fragment by washing the support after the incubation carried out in step (b); and (d) analyzing by an ELISA technique to detect the presence or absence of ArsR protein remaining attached to the DNA fragment.

Abstract: The subject invention pertains to an assay and a method for diagnosing, identifying and/or differentiating microorganisms, and in particular bacteria such as Mycobacterium spp. within biological samples. The present invention also relates to assays, gene arrays, probes and primers, nucleic acids and methods for detecting microorganisms in a sample.

Abstract: Invention is using M. brumae is a mycobacterium strain which stimulates immune system cells strongly, is non-pathogen for humans and has all of the defining attributes of the strain with catalog number 51384, American Type Culture Collection (ATCC) for therapy of superficial bladder cancers.

Abstract: The present invention relates to methods and systems for scanning, detecting, and monitoring microorganisms on solid or semi-solid media using intrinsic fluorescence (IF) measurements. The methods are further directed to detection, characterization and/or identification of microorganisms on a solid or semi-solid media using intrinsic fluorescence (IF) measurements that are characteristic of said microorganisms.

Abstract: The invention relates to a method for determining the presence and/or amount of viable cells in a liquid sample.

Abstract: Provided herein are improved methods of characterizing antibiotic agents according to the effect the antibiotic agent has on a bacterial cell. This allows for rapid screening of potential antibiotic agents, e.g., for improved antibiotics, and classification of antibiotic agents. The present techniques also allow for profiling of bacterial strains for susceptibility of antibiotic agents and, e.g., determining which are most susceptible to particular modes of action.

Abstract: A compound useful as an antifungal agent, particularly a therapeutic agent for deep-seated mycoses, is provided. A fungus Acremonium persicinum was collected, and cyclic compounds were isolated from culture liquids thereof. The present inventors confirmed that the cyclic compounds or salts thereof have a potent antifungal activity and are useful as medicaments, particularly an antifungal agent, and thus the present invention was completed. The cyclic compound and the salt thereof according to the present invention can be used as an agent for preventing or treating mycoses, particularly deep-seated mycoses.

Abstract: There is provided a method for the detection and identification of infection of a subject by a microorganism, wherein the method is based on the use of small RNA derived sequences and subtraction and assembly thereof.

Abstract: The present invention relates to a non-toxic dipolar solvent for chromogenic substrate for detecting presence of lacZ gene and/or gene activity, which comprises a stabilizing amount of a solubilizing agent. The present invention also relates to a method for inducing lac operon in screening assay, comprising the step of contacting an agar plate with at least one essential oil in a concentration sufficient to induce the lac operon. The present invention further relates to a method for detecting the presence of bacteria, comprising the step of contacting an agar plate with at least one essential oil in a concentration sufficient to induce detection of the bacteria.

Abstract: The invention relates to a cell capture system for use in determining the presence and/or amount of cells, for example, viable cells, in a liquid sample, and to methods of using such a cell capture system.

Abstract: The present invention relates to a method for detecting at least one microorganism in a sample, including: cultivating the sample in a liquid medium in the presence of at least one specific ligand of the microorganism, and at least one scavenger having a lower affinity to the microorganism than the ligand, the binding of a compound to the ligand producing a first measurable signal and the binding of a compound to the scavenger producing a second measurable signal; determining the values of the first and second signals for at least one cultivation period; wherein it is deduced that the sample includes the microorganism when the values of the first signal and second signal are different for the same cultivation period.

Abstract: The invention generally relates to methods of using compositions that include sets of magnetic particles, members of each set being conjugated to an antibody specific for a pathogen, and magnets to isolate a pathogen from a body fluid sample.

Abstract: This invention relates to novel nucleic acid probes and methods for detecting Plasmodium parasites as well as detecting different Plasmodium parasites selectively from one another.