Bacterial Glutamine Synthetases as a Novel Metabolic Selection Marker to Improve CHO Cell Culture Performance Through Selection Stringency Modulation.

The use of metabolic selection markers has advanced stable cell line generation, increasing productivity while simultaneously eliminating the need for antibiotic reagents. This study explores the potential of bacterially derived glutamine synthetases (GS) as a novel generation of metabolic selection markers to further enhance CHO cell culture performance. GS-I proteins were extracted from the genomes of enterobacterial and actinomycetes species.

Q-functions, synchronization, and Arnold tongues for coupled stochastic oscillators.

Phase reduction is an effective theoretical and numerical tool for studying the synchronization of coupled deterministic oscillators. Stochastic oscillators require new definitions of the asymptotic phase. The Q-function, i.

AAV yield, bioactivity, and particle heterogeneity are impacted by genome size and non-coding DNA elements.

Adeno-associated virus (AAV) vectors currently represent the most attractive platform for therapeutic gene delivery. Ensuring efficient AAV production and vector integrity, defined by efficient packaging of full-size genomes, high full/empty ratios, and optimal bioactivity, therefore is of utmost importance. However, during AAV production, not only capsids that carry the full-size genome but also empty as well as capsids containing partial or oversized genomes are produced.

Extraction of parameters of a stochastic integrate-and-fire model with adaptation from voltage recordings.

Integrate-and-fire models are an important class of phenomenological neuronal models that are frequently used in computational studies of single neural activity, population activity, and recurrent neural networks. If these models are used to understand and interpret electrophysiological data, it is important to reliably estimate the values of the model's parameters. However, there are no standard methods for the parameter estimation of Integrate-and-fire models.

Self-consistent autocorrelation of a disordered Kuramoto model in the asynchronous state.

The Kuramoto model has provided deep insights into synchronization phenomena and remains an important paradigm to study the dynamics of coupled oscillators. Yet, despite its success, the asynchronous regime in the Kuramoto model has received limited attention. Here, we adapt and enhance the mean-field approach originally proposed by Stiller and Radons [Phys.

Effect of burst spikes on linear and nonlinear signal transmission in spiking neurons.

We study the impact of bursts on spike statistics and neural signal transmission. We propose a stochastic burst algorithm that is applied to a burst-free spike train and adds a random number of temporally-jittered burst spikes to each spike. This simple algorithm ignores any possible stimulus-dependence of bursting but allows to relate spectra and signal-transmission characteristics of burst-free and burst-endowed spike trains.

The fluctuation-dissipation relation holds for a macroscopic tracer in an active bath.

The fluctuation-dissipation relation (FDR) links thermal fluctuations and dissipation at thermal equilibrium through temperature. Extending it beyond equilibrium conditions in pursuit of broadening thermodynamics is often feasible, albeit with system-dependent specific conditions. We demonstrate experimentally that a generalized FDR holds for a harmonically trapped tracer colliding with self-propelled walkers.

Noise intensity of a Markov chain.

Stochastic transitions between discrete microscopic states play an important role in many physical and biological systems. Often these transitions lead to fluctuations on a macroscopic scale. A classic example from neuroscience is the stochastic opening and closing of ion channels and the resulting fluctuations in membrane current.

Nature as blueprint: Global phenotype engineering of CHO production cells based on a multi-omics comparison with plasma cells.

Especially for the production of artificial, difficult to express molecules a further development of the CHO production cell line is required to keep pace with the continuously increasing demands. However, the identification of novel targets for cell line engineering to improve CHO cells is a time and cost intensive process. Since plasma cells are evolutionary optimized for a high antibody expression in mammals, we performed a comprehensive multi-omics comparison between CHO and plasma cells to exploit optimized cellular production traits.

Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations.

Hippocampal ripple oscillations have been implicated in important cognitive functions such as memory consolidation and planning. Multiple computational models have been proposed to explain the emergence of ripple oscillations, relying either on excitation or inhibition as the main pacemaker. Nevertheless, the generating mechanism of ripples remains unclear.

Fluctuation-response relations for integrate-and-fire models with an absolute refractory period.

We study the problem of relating the spontaneous fluctuations of a stochastic integrate-and-fire (IF) model to the response of the instantaneous firing rate to time-dependent stimulation if the IF model is endowed with a non-vanishing refractory period and a finite (stereotypical) spike shape. This seemingly harmless addition to the model is shown to complicate the analysis put forward by Lindner Phys. Rev.

In pursuit of a minimal CHO genome: Establishment of large-scale genome deletions.

Chinese hamster ovary (CHO) cells are the most commonly used mammalian cell line for the production of complex therapeutic glycoproteins. As CHO cells have evolved as part of a multicellular organism, they harbor many cellular functions irrelevant for their application as production hosts in industrial bioprocesses. Consequently, CHO cells have been the target for numerous genetic engineering efforts in the past, but a tailored host cell chassis holistically optimized for its specific task in a bioreactor is still missing.

An integrate-and-fire approach to Ca signaling. Part II: Cumulative refractoriness.

Inositol 1,4,5-trisphosphate-induced Ca signaling is a second messenger system used by almost all eukaryotic cells. The agonist concentration stimulating Ca signals is encoded in the frequency of a Ca concentration spike sequence. When a cell is stimulated, the interspike intervals (ISIs) often show a distinct transient during which they gradually increase, a system property we refer to as cumulative refractoriness.

Detecting a periodic signal by a population of spiking neurons in the weakly nonlinear response regime.

Motivated by experimental observations, we investigate a variant of the cocktail party problem: the detection of a weak periodic stimulus in the presence of fluctuations and another periodic stimulus which is stronger than the periodic signal to be detected. Specifically, we study the response of a population of stochastic leaky integrate-and-fire (LIF) neurons to two periodic signals and focus in particular on the question, whether the presence of one of the stimuli can be detected from the population activity. As a detection criterion, we use a simple threshold-crossing of the population activity over a certain time window.

Droplet digital PCR: A comprehensive tool for genetic analysis and prediction of bispecific antibody assembly during cell line development.

Molecular biological methods have emerged as inevitable tools to accompany the process of cell line development for the generation of stable and highly productive manufacturing cell lines in the biopharmaceutical industry. PCR-based methods are especially useful for screening and characterization of cell lines due to their low cost, scalability, precision and propensity for multidimensional read-outs. In this study, the diverse applications of droplet digital PCR (ddPCR) as a molecular biological tool for cell line development are demonstrated.

A universal description of stochastic oscillators.

Many systems in physics, chemistry, and biology exhibit oscillations with a pronounced random component. Such stochastic oscillations can emerge via different mechanisms, for example, linear dynamics of a stable focus with fluctuations, limit-cycle systems perturbed by noise, or excitable systems in which random inputs lead to a train of pulses. Despite their diverse origins, the phenomenology of random oscillations can be strikingly similar.

Modeling IP-induced Ca signaling based on its interspike interval statistics.

Inositol 1,4,5-trisphosphate (IP)-induced Ca signaling is a second messenger system used by almost all eukaryotic cells. Recent research demonstrated randomness of Ca signaling on all structural levels. We compile eight general properties of Ca spiking common to all cell types investigated and suggest a theory of Ca spiking starting from the random behavior of IP receptor channel clusters mediating the release of Ca from the endoplasmic reticulum capturing all general properties and pathway-specific behavior.

Theory of the asynchronous state of structured rotator networks and its application to recurrent networks of excitatory and inhibitory units.

Recurrently coupled oscillators that are sufficiently heterogeneous and/or randomly coupled can show an asynchronous activity in which there are no significant correlations among the units of the network. The asynchronous state can nevertheless exhibit a rich temporal correlation statistics that is generally difficult to capture theoretically. For randomly coupled rotator networks, it is possible to derive differential equations that determine the autocorrelation functions of the network noise and of the single elements in the network.

Active Brownian particles in a biased periodic potential.

We study transport properties of an active Brownian particle with an Rayleigh-Helmholtz friction function in a biased periodic potential. In the absence of noise and depending on the parameters of the friction function and on the bias force, the motion of the particle can be in a locked state or in different running states. According to the type of solutions, the parameter plane of friction and bias force can be divided into four regions.

Deciphering integration loci of CHO manufacturing cell lines using long read nanopore sequencing.

Despite advances in genetic characterization of Chinese hamster ovary (CHO) cell lines regarding identification of integration sites using next generation sequencing, e.g. targeted locus amplification sequencing (TLA-seq), the concatemer structure of the integrated vectors remains elusive.

An integrate-and-fire approach to Ca signaling. Part I: Renewal model.

In computational neuroscience integrate-and-fire models capture the spike generation by a subthreshold dynamics supplemented by a simple fire-and-reset rule; they allow for a numerically efficient and analytically tractable description of stochastic single cell as well as network dynamics. Stochastic spiking is also a prominent feature of Ca signaling which suggests to adopt the integrate-and-fire approach for this fundamental biophysical process. The model introduced here consists of two components describing 1) activity of clusters of inositol-trisphosphate receptor channels and 2) dynamics of the global Ca concentrations in the cytosol.

Fluctuation-Dissipation Relations for Spiking Neurons.

Spontaneous fluctuations and stimulus response are essential features of neural functioning, but how they are connected is poorly understood. I derive fluctuation-dissipation relations (FDR) between the spontaneous spike and voltage correlations and the firing rate susceptibility for (i) the leaky integrate-and-fire (IF) model with white noise and (ii) an IF model with arbitrary voltage dependence, an adaptation current, and correlated noise. The FDRs can be used to derive thus far unknown statistics analytically [model (i)] or the otherwise inaccessible intrinsic noise statistics [model (ii)].

The steady state and response to a periodic stimulation of the firing rate for a theta neuron with correlated noise.

The stochastic activity of neurons is caused by various sources of correlated fluctuations and can be described in terms of simplified, yet biophysically grounded, integrate-and-fire models. One paradigmatic model is the quadratic integrate-and-fire model and its equivalent phase description by the theta neuron. Here we study the theta neuron model driven by a correlated Ornstein-Uhlenbeck noise and by periodic stimuli.