Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.

Abstract: The present invention relates to compositions which may comprise a molecular sled linked to cargo and uses thereof. In particular, the present invention relates to a non-naturally occurring or engineered composition which may comprise a molecular sled, linkers and a molecular cargo connected to the sled via the linkers. Methods involving the use of molecular sleds and their cargoes and pharmaceutical compositions, methods for treating treating cancer, a degenerative disease, a genetic disease or an infectious disease as well as diagnostic methods are also contemplated by the present invention.

Abstract: An illumination system is disclosed for providing dual-excitation wavelength illumination for non-linear optical microscopy and micro-spectroscopy. The illumination system includes a laser system, an optical splitting means, a frequency shifting system, and a picosecond amplifier system. The laser system includes a laser for providing a first train of pulses at a center optical frequency ?1. The optical splitting means divides the first train of pulses at the center optical frequency ?1 into two trains of pulses. The frequency shifting system shifts the optical frequency of one of the two trains of pulses to provide a frequency shifted train of pulses. The picosecond amplifier system amplifies the frequency shifted train of pulses to provide an amplified frequency-shifted train of pulses having a pulse duration of at least 0.5 picoseconds.

Abstract: An illumination system is disclosed for providing dual-excitation wavelength illumination for non-linear optical microscopy and micro-spectroscopy. The illumination system includes a laser system, an optical splitting means, a frequency shifting system, and a picosecond amplifier system. The laser system includes a laser for providing a first train of pulses at a center optical frequency ?1. The optical splitting means divides the first train of pulses at the center optical frequency ?1 into two trains of pulses. The frequency shifting system shifts the optical frequency of one of the two trains of pulses to provide a frequency shifted train of pulses. The picosecond amplifier system amplifies the frequency shifted train of pulses to provide an amplified frequency-shifted train of pulses having a pulse duration of at least 0.5 picoseconds.

Abstract: Methods and compositions for amplifying the whole genome of a single cell are provided.

Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.

Abstract: In general, the invention features methods and systems for sequencing of nucleic acids based on the measurement of the incorporation of fluorogenic nucleotides in microreactors. The invention provides numerous advantages over previous systems such as unambiguous determination of sequence, fast cycle time, long read lengths, low overall cost of reagents, low instrument cost, and high throughput. The invention also features methods and kits for nucleic acid amplification. The amplification and sequencing aspects of the invention may or may not be employed in conjunction with one another. The invention also features fluorogenic nucleotides that may be used in the sequencing methods of the invention.

Abstract: A microscopy imaging system includes a first light source for providing a first train of pulses at a first center optical frequency ?1, a second light source for providing a second train of pulses at a second center optical frequency ?2, a modulator system, an optical detector, and a processor. The modulator system is for modulating a beam property of the second train of pulses at a modulation frequency f of at least 100 kHz. The optical detector is for detecting an integrated intensity of substantially all optical frequency components of the first train of pulses from the common focal volume by blocking the second train of pulses being modulated. The processor is for detecting, a modulation at the modulation frequency f, of the integrated intensity of the optical frequency components of the first train of pulses to provide a pixel of an image for the microscopy imaging system.

Abstract: A microscopy imaging system is disclosed that includes a light source system, focusing optics, an optical detector and a processor. The light source system is for providing an excitation beam at a center optical frequency ?e and for providing a stimulation beam at a center optical frequency ?s. The focusing optics is for directing and focusing the excitation beam toward a common focal volume such that a sample may be excited to an electronic excited state, and for directing and focusing the stimulation beam toward the common focal volume such that stimulated emission induced from the electronic excited state results in an increase in intensity of the stimulated beam. The optical detector is for detecting an increase in a radiation field at the center optical frequency ?s from stimulated emission from the common focal volume and for providing a detector signal. The processor is for receiving the detector signal and for providing a pixel of an image for the microscopy imaging system.

Abstract: Disclosed herein are methods and compositions for continuous single-molecule nucleic acid sequencing by synthesis with fluorogenic nucleotides.

Abstract: A microscopy imaging system is disclosed that includes a light source system, a spectral shaper, a modulator system, an optics system, an optical detector and a processor. The light source system is for providing a first train of pulses and a second train of pulses. The spectral shaper is for spectrally modifying an optical property of at least some frequency components of the broadband range of frequency components such that the broadband range of frequency components is shaped producing a shaped first train of pulses to specifically probe a spectral feature of interest from a sample, and to reduce information from features that are not of interest from the sample. The modulator system is for modulating a property of at least one of the shaped first train of pulses and the second train of pulses at a modulation frequency.

Abstract: A microscopy imaging system is disclosed that includes a first light source, a second light source, a modulator system, focusing optics, an optical detector, and a processor. The first light source is for providing a first train of pulses at a first center optical frequency ?1. The second light source is for providing a second train of pulses at a second center optical frequency ?2 such that a difference between ?1 and ?2 is resonant with a vibrational frequency of a sample in the focal volume. The second train of pulses is temporally synchronized with the first train of pulses. The modulator system is for modulating a beam property of the second train of pulses at a modulation frequency f of at least 100 kHz. The focusing optics is for directing and focusing the first train of pulses and the second train of pulses toward a common focal volume.

Abstract: The invention features compositions, methods, and systems for single-molecule sequencing of nucleic acids based on the continuous measurement of the incorporation of fluorogenic nucleotides in microreactors. In particular, the invention features fluorogenic compounds for use in nucleic acid sequencing. The invention provides numerous advantages over previous systems such as unambiguous determination of sequence, continuous sequencing, long read lengths, low overall cost, and ease of sample preparation.

Abstract: A system is disclosed for providing a first electromagnetic field and a second electromagnetic field to vibrational analysis equipment that is responsive to a difference between first and second frequencies of the first and second electromagnetic fields respectively. The system includes a non-linear crystal that may be pumped at a high repetition rate to provide a pulsed signal field at a signal field frequency and a pulsed idler field at an idler field frequency as output. The signal field provides the first electromagnetic field and the idler field provides the second electromagnetic field. The system also includes a tuning system for permitting the difference between the signal field frequency and the idler field frequency to be changed. The system also includes an output unit for providing the first and second electromagnetic fields to the vibrational analysis equipment.

Abstract: The invention provides a system and method for automatic real-time monitoring for the presence of a pathogen in water using coherent anti-stokes Raman scattering (CARS) microscopy. Water sample trapped in a trapping medium is provided to a CARS imager. CARS images are provided to a processor for automatic analyzing for the presence of image artifacts having pre-determined features characteristic to the pathogen. If a match is found, a CARS spectrum is taken and compared to a stored library of reference pathogen-specific spectra for pathogen identification. The system enables automatic pathogen detection in flowing water in real time.

Abstract: A system is disclosed for detecting a signal field from a sample volume. The system includes a source system and an optical fiber system. The source system provides a first electromagnetic field at a first frequency and a second electromagnetic field at a second frequency that is different from the first frequency. The optical fiber system includes at least one optical fiber for guiding the first and second electromagnetic fields to the sample volume to generate coherent radiation characteristic of molecular vibrations by non-linear interaction of the first and second fields with the sample volume. The optical fiber system also receives the signal field resulting from the coherent radiation, and guides the signal field to a detector.

Abstract: A system is disclosed for detecting a non-linear coherent field induced in a sample volume. The system includes a first source for generating a first electromagnetic field at a first frequency, a second source for generating a second electromagnetic field at a second frequency, first optics for directing the first and second electromagnetic fields toward the sample volume, second optics for directing the first and second electromagnetic fields toward a local oscillator volume, and an interferometer. The interferometer is for interfering a first scattering field that is generated by the interaction of the first and second electromagnetic fields in the sample volume, with a second scattering field that is generated by the interaction of the first and second electromagnetic fields in the local oscillator volume.

Abstract: A system is disclosed for detecting a nonlinear coherent field induced in a sample. The system includes optics, a modulation system, and a detector system. The optics are for directing a first electromagnetic field at a first frequency ?1 and a second electromagnetic field at a second frequency ?2 toward a focal volume such that a difference frequency ?1–?2 is resonant with a vibrational frequency of a sample in the focal volume. The modulation system is for modulating the difference frequency ?1–?2 such that the difference frequency ?1–?2 is tuned in and out of the vibrational frequency of the sample of at a modulation frequency. The detector system is for detecting an optical field that is generated through non-linear interaction of ?1 and ?2 and the sample responsive to the modulation frequency.

Abstract: Systems and methods are disclosed for detecting a coherent anti-Stokes Raman scattering (CARS) signal from a microscopic sample in an epi-direction. In an embodiment, the system includes at least two sources having a pump source for generating a pump field at the pump frequency, a Stoke source for generating a Stoke field at the Stoke frequency that is different from the pump frequency, optics (64) for directing the pump and Stoke beams (60) in a collinear fashion through a focusing lens (66) toward a common focal spot in a sample (70), and detector optics that images the CARS in epi-direction, which is generated by the interaction of the pump and Stoke fields (60) with the sample (70) and is collected by the same focusing lens (66), towards an epi-detector (78).

Abstract: Systems and methods are disclosed for detecting a nonlinear coherent field induced in a microscopic sample. The system includes in an embodiment, a first source for generating a first polarized electromagnetic field at a first frequency and a second source for generating a second polarized electromagnetic field at a second frequency that is different from the first frequency. The system further includes optics for combining the first polarized electromagnetic field and the second polarized electromagnetic field in a collinear fashion such that the difference in polarization angles is &phgr; wherein &phgr; is not equal to zero. The optics further direct the combined electromagnetic field toward a common focal volume. The system also includes a polarization sensitive detector for detecting a nonlinear coherent field that is generated responsive to the first and second polarized electromagnetic fields in the focal volume.