Exploring metabolic effects of dipeptide feed media on CHO cell cultures by in silico model-guided flux analysis.

There is a growing interest in perfusion or continuous processes to achieve higher productivity of biopharmaceuticals in mammalian cell culture, specifically Chinese hamster ovary (CHO) cells, towards advanced biomanufacturing. These intensified bioprocesses highly require concentrated feed media in order to counteract their dilution effects. However, designing such condensed media formulation poses several challenges, particularly regarding the stability and solubility of specific amino acids.

Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses.

Designing and selecting cell culture media along with their feeding are a key strategy to maximize culture performance in biopharmaceutical processes. However, the sensitivity of mammalian cells to their culture environment necessitates specific nutritional requirements for their growth and the production of high-quality proteins such as antibodies, depending on the cell lines and operational conditions employed. In this regard, previously we developed a data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design and reformulate basal media.

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation.

Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation.

Data-driven and model-guided systematic framework for media development in CHO cell culture.

Proposed herein is a systematic media design framework that combines multivariate statistical approaches with in silico analysis of a genome-scale metabolic model of Chinese hamster ovary cell. The framework comprises sequential modules including cell culture and metabolite data collection, multivariate data analysis, in silico modeling and flux prediction, and knowledge-based identification of target media components. Two monoclonal antibody-producing cell lines under two different media conditions were used to demonstrate the applicability of the framework.

Exodus: sequencing-based pipeline for quantification of pooled variants.

Summary: Next-Generation Sequencing is widely used as a tool for identifying and quantifying microorganisms pooled together in either natural or designed samples. However, a prominent obstacle is achieving correct quantification when the pooled microbes are genetically related. In such cases, the outcome mostly depends on the method used for assigning reads to the individual targets.

Single beam low frequency 2D Raman spectroscopy.

Low frequency Raman spectroscopy resolves the slow vibrations resulting from collective motions of molecular structures. This frequency region is extremely challenging to access via other multidimensional methods such as 2D-IR. In this paper, we describe a new scheme which measures 2D Raman spectra in the low frequency regime.

Light focusing through scattering media via linear fluorescence variance maximization, and its application for fluorescence imaging.

We demonstrate focusing and imaging through a scattering medium without access to the fluorescent object by using wavefront shaping. Our concept is based on utilizing the spatial fluorescence contrast which naturally exists in the hidden target object. By scanning the angle of incidence of the illuminating laser beam and maximizing the variation of the detected fluorescence signal from the object, as measured by a bucket detector at the front of the scattering medium, we are able to generate a tightly focused excitation spot.

Simplified approach to low-frequency coherent anti-Stokes Raman spectroscopy using a sharp spectral edge filter.

Coherent anti-Stokes Raman scattering (CARS) has found wide applications in biomedical research. Compared with alternatives, single-beam CARS is especially attractive at low frequencies. Yet, currently existing schemes necessitate a relatively complicated setup to perform high-resolution spectroscopy.

Observation of Stimulated Hawking Radiation in an Optical Analogue.

The theory of Hawking radiation can be tested in laboratory analogues of black holes. We use light pulses in nonlinear fiber optics to establish artificial event horizons. Each pulse generates a moving perturbation of the refractive index via the Kerr effect.

Revealing true coupling strengths in two-dimensional spectroscopy with sparsity-based signal recovery.

Two-dimensional (2D) spectroscopy is used to study the interactions between energy levels in both the field of optics and nuclear magnetic resonance (NMR). Conventionally, the strength of interaction between two levels is inferred from the value of their common off-diagonal peak in the 2D spectrum, which is termed the cross peak. However, stronger diagonal peaks often have long tails that extend into the locations of the cross peaks and alter their values.

Mode conversion via wavefront shaping.

In recent years, wavefront shaping has been utilized to control and correct distorted light for enhancing a bright spot, generation of a Bessel beam or darkening a complete area at the output of a scattering system. All these outcomes can be thought of as enhancing a particular mode of the output field. In this letter, we study the relation between the attainable enhancement factor, corresponding to the efficiency of mode conversion, and the field distribution of the target mode.

Impulsive Raman spectroscopy via precision measurement of frequency shift with low energy excitation.

Stimulated Raman scattering (SRS) has recently become useful for chemically selective bioimaging. It is usually measured via modulation transfer from the pump beam to the Stokes beam. Impulsive stimulated Raman spectroscopy, on the other hand, relies on the spectral shift of ultrashort pulses as they propagate in a Raman active sample.

Computational modeling of three-dimensional ECM-rigidity sensing to guide directed cell migration.

Filopodia have a key role in sensing both chemical and mechanical cues in surrounding extracellular matrix (ECM). However, quantitative understanding is still missing in the filopodial mechanosensing of local ECM stiffness, resulting from dynamic interactions between filopodia and the surrounding 3D ECM fibers. Here we present a method for characterizing the stiffness of ECM that is sensed by filopodia based on the theory of elasticity and discrete ECM fiber.

A New Cell Separation Method Based on Antibody-Immobilized Nanoneedle Arrays for the Detection of Intracellular Markers.

Focusing on intracellular targets, we propose a new cell separation technique based on a nanoneedle array (NNA) device, which allows simultaneous insertion of multiple needles into multiple cells. The device is designed to target and lift ("fish") individual cells from a mixed population of cells on a substrate using an antibody-functionalized NNA. The mechanics underlying this approach were validated by force analysis using an atomic force microscope.

GLADIATOR: a global approach for elucidating disease modules.

Background: Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based approaches for deciphering disease mechanisms. In particular, protein-protein interaction networks were successfully used to illuminate disease modules, i.

Quantum correlation enhanced super-resolution localization microscopy enabled by a fibre bundle camera.

Despite advances in low-light-level detection, single-photon methods such as photon correlation have rarely been used in the context of imaging. The few demonstrations, for example of subdiffraction-limited imaging utilizing quantum statistics of photons, have remained in the realm of proof-of-principle demonstrations. This is primarily due to a combination of low values of fill factors, quantum efficiencies, frame rates and signal-to-noise characteristic of most available single-photon sensitive imaging detectors.

Weakly diverging to tightly focused Gaussian beams: a single set of analytic expressions: continuation-symmetric beams.

The always diverging-converging laser beams, more rigorously referred to as Gaussian beams, are part of many physical and electro-optical systems. Obviously, a single set of analytic expressions describing these beams in a large span of divergence-convergence angles at the focal plane, and at any distance away from the focal plane, will prove very handy. We have recently published three such analytic sets, one set for linearly polarized beams and two sets for radially polarized beams.

Weakly diverging to tightly focused Gaussian beams: a single set of analytic expressions.

Analytic expressions describing all vector components of Gaussian beams, linearly polarized as well as radially polarized, are presented. These simple expressions, to high powers in divergence angle, were derived from a single-component vector potential. The vector potential itself, as in the 1979 work of Davis [Phys.

High efficiency penetration of antibody-immobilized nanoneedle thorough plasma membrane for in situ detection of cytoskeletal proteins in living cells.

Background: The field of structural dynamics of cytoskeletons in living cells is gathering wide interest, since better understanding of cytoskeleton intracellular organization will provide us with not only insights into basic cell biology but may also enable development of new strategies in regenerative medicine and cancer therapy, fields in which cytoskeleton-dependent dynamics play a pivotal role. The nanoneedle technology is a powerful tool allowing for intracellular investigations, as it can be directly inserted into live cells by penetrating through the plasma membrane causing minimal damage to cells, under the precise manipulation using atomic force microscope. Modifications of the nanoneedles using antibodies have allowed for accurate mechanical detection of various cytoskeletal components, including actin, microtubules and intermediate filaments.

Mechanoporation of living cells for delivery of macromolecules using nanoneedle array.

Efficient and rapid delivery of macromolecule probes, such as quenchbodies and other large biomarkers that cannot readily pass through the plasma membrane, is necessary for live-cell imaging and other intracellular analyses. We present here an alternative, simple method for delivery of macromolecules into live cells. In this method, which we term here mechanoporation, a nanoneedle array is used for making transient pores in the plasma membrane to allow access of desired macromolecules into thousands of live cells, simultaneously.

Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans.

Understanding the genetic basis underlying individual responses to drug treatment is a fundamental task with implications to drug development and administration. Pharmacogenomics is the study of the genes that affect drug response. The study of pharmacogenomic associations between a drug and a gene that influences the interindividual drug response, which is only beginning, holds much promise and potential.

Second and third harmonic waves excited by focused Gaussian beams.

Harmonic generation by tightly-focused Gaussian beams is finding important applications, primarily in nonlinear microscopy. It is often naively assumed that the nonlinear signal is generated predominantly in the focal region. However, the intensity of Gaussian-excited electromagnetic harmonic waves is sensitive to the excitation geometry and to the phase matching condition, and may depend on quite an extended region of the material away from the focal plane.

Oscillating high-aspect-ratio monolithic silicon nanoneedle array enables efficient delivery of functional bio-macromolecules into living cells.

Delivery of biomolecules with use of nanostructures has been previously reported. However, both efficient and high-throughput intracellular delivery has proved difficult to achieve. Here, we report a novel material and device for the delivery of biomacromolecules into live cells.