Exploring a role for flow-induced aggregation assays in platform formulation optimisation for antibody-based proteins.

The development time of therapeutic monoclonal antibodies (mAbs) has been shortened by formulation platforms and the assessment of 'protein stability' using 'developability' assays. A range of assays are used to measure stability to a variety of stresses, including forces induced by hydrodynamic flow. We have previously developed a low-volume Extensional Flow Device (EFD) which subjects proteins to defined fluid flow fields in the presence of glass interfaces and used it to identify robust candidate sequences.

Peculiar -mer Spectra Are Correlated with 3D Contact Frequencies and Breakpoint Regions in the Human Genome.

Background: It is widely accepted that the 3D chromatin organization in human cell nuclei is not random and recent investigations point towards an interactive relation of epigenetic functioning and chromatin (re-)organization. Although chromatin organization seems to be the result of self-organization of the entirety of all molecules available in the cell nucleus, a general question remains open as to what extent chromatin organization might additionally be predetermined by the DNA sequence and, if so, if there are characteristic differences that distinguish typical regions involved in dysfunction-related aberrations from normal ones, since typical DNA breakpoint regions involved in disease-related chromosome aberrations are not randomly distributed along the DNA sequence.

Methods: Highly conserved -mer patterns in intronic and intergenic regions have been reported in eukaryotic genomes.

Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes.

The specific characteristics of words (2 ≤ k ≤ 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (≤12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome.

Experimental study of intrinsic localized mode mobility in a cyclic, balanced, 1D nonlinear transmission line.

Mobile intrinsic localized modes (ILMs) in balanced nonlinear capacitive-inductive cyclic transmission lines are studied by experiment, using a spatiotemporal driver under damped steady-state conditions. Without nonlinear balance, the experimentally observed resonance between the traveling ILM and normal modes of the nonlinear transmission line generates lattice drag via the production of a lattice backwave. In our experimental study of a balanced running ILM in a steady state, it is observed that the fundamental resonance can be removed over extended, well-defined driving frequency intervals and strongly suppressed over the complete ILM driving frequency range.

Propagating intrinsic localized mode in a cyclic, dissipative, self-dual one-dimensional nonlinear transmission line.

A well-known feature of a propagating localized excitation in a discrete lattice is the generation of a backwave in the extended normal mode spectrum. To quantify the parameter-dependent amplitude of such a backwave, the properties of a running intrinsic localized mode (ILM) in electric, cyclic, dissipative, nonlinear 1D transmission lines, containing balanced nonlinear capacitive and inductive terms, are studied via simulations. Both balanced and unbalanced damping and driving conditions are treated.

Hybrid leaching of tantalum and other valuable metals from tantalum capacitor waste.

We propose a novel integrated model for the recovery of tantalum from tantalum-rich waste using a combination of hydrometallurgical and bio-metallurgical processes. To this end, leaching experiments with heterotrophs (Pseudomonas putida, Bacillus subtilis and Penicillium simplicissimum) were carried out. The heterotrophic fungal strain leached manganese with an efficiency of 98%; however, no tantalum was detected in the leachate.

Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes.

Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g.

Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change.

Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers.

Chemical and Microbial Leaching of Valuable Metals from PCBs and Tantalum Capacitors of Spent Mobile Phones.

We compared chemical and microbial leaching for multi-metal extraction from printed circuit boards (PCBs) and tantalum capacitor scrap. A mixed consortium of acidophiles and heterotrophic fungal strains were used in the experiments and compared to chemical leaching using specific acids (sulfuric, citric and oxalic acids). Under optimum conditions, 100% extraction efficiency of Cu, and nearly 85% of Zn, Fe, Al and Ni were achieved from PCB and tantalum capacitor scrap samples using sulfuric acid.

Experimental investigation of supertransmission for an intrinsic localized mode in a cyclic nonlinear transmission line.

In this experimental study of the nonlinear loss mechanism between traveling localized excitation and the underlying extended normal mode spectrum for a 1D lattice, three types of cyclic, electric, nonlinear transmission lines (NLTLs) are used. They are nonlinear capacitive, inductive, and capacitive+inductive NLTLs. To maintain a robust, steady-state traveling intrinsic localized mode (ILM), a traveling wave driver is used.

Eukaryotic Genomes Show Strong Evolutionary Conservation of -mer Composition and Correlation Contributions between Introns and Intergenic Regions.

Several strongly conserved DNA sequence patterns in and between introns and intergenic regions (IIRs) consisting of short tandem repeats (STRs) with repeat lengths <3 bp have already been described in the kingdom of . In this work, we expanded the search and analysis of conserved DNA sequence patterns to a wider range of genomes. Our aims were to confirm the conservation of these patterns, to support the hypothesis on their functional constraints and/or the identification of unknown patterns.

Fc-GDF15 glyco-engineering and receptor binding affinity optimization for body weight regulation.

GDF15 is a distant TGF-β family member that induces anorexia and weight loss. Due to its function, GDF15 has attracted attention as a potential therapeutic for the treatment of obesity and its associated metabolic diseases. However, the pharmacokinetic and physicochemical properties of GDF15 present several challenges for its development as a therapeutic, including a short half-life, high aggregation propensity, and protease susceptibility in serum.

Genetic rearrangement during site specific integration event facilitates cell line development of a bispecific molecule.

Site specific integration (SSI) expression systems offer robust means of generating highly productive and stable cell lines for traditional monoclonal antibodies. As complex modalities such as antibody-like molecules comprised of greater than two peptides become more prevalent, greater emphasis needs to be placed on the ability to produce appreciable quantities of the correct product of interest (POI). The ability to screen several transcript stoichiometries could play a large role in ensuring high amounts of the correct POI.

COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes.

During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target.

Structure-function relationships of the soluble form of the antiaging protein Klotho have therapeutic implications for managing kidney disease.

The fortuitously discovered antiaging membrane protein αKlotho (Klotho) is highly expressed in the kidney, and deletion of the gene in mice causes a phenotype strikingly similar to that of chronic kidney disease (CKD). Klotho functions as a co-receptor for fibroblast growth factor 23 (FGF23) signaling, whereas its shed extracellular domain, soluble Klotho (sKlotho), carrying glycosidase activity, is a humoral factor that regulates renal health. Low sKlotho in CKD is associated with disease progression, and sKlotho supplementation has emerged as a potential therapeutic strategy for managing CKD.

Transient CHO expression platform for robust antibody production and its enhanced N-glycan sialylation on therapeutic glycoproteins.

Large-scale transient expression in mammalian cells is a rapid protein production technology often used to shorten overall timelines for biotherapeutics drug discovery. In this study we demonstrate transient expression in a Chinese hamster ovary (CHO) host (ExpiCHO-S™) cell line capable of achieving high recombinant antibody expression titers, comparable to levels obtained using human embryonic kidney (HEK) 293 cells. For some antibodies, ExpiCHO-S™ cells generated protein materials with better titers and improved protein quality characteristics (i.

Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes.

In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets.

Clustering the Orion B giant molecular cloud based on its molecular emission.

Context: Previous attempts at segmenting molecular line maps of molecular clouds have focused on using position-position-velocity data cubes of a single molecular line to separate the spatial components of the cloud. In contrast, wide field spectral imaging over a large spectral bandwidth in the (sub)mm domain now allows one to combine multiple molecular tracers to understand the different physical and chemical phases that constitute giant molecular clouds (GMCs).

Aims: We aim at using multiple tracers (sensitive to different physical processes and conditions) to segment a molecular cloud into physically/chemically similar regions (rather than spatially connected components), thus disentangling the different physical/chemical phases present in the cloud.

Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure.

Immunostaining and fluorescence in situ hybridization (FISH) are well established methods for specific labelling of chromatin in the cell nucleus. COMBO-FISH (combinatorial oligonucleotide fluorescence in situ hybridization) is a FISH method using computer designed oligonucleotide probes specifically co-localizing at given target sites. In combination with super resolution microscopy which achieves spatial resolution far beyond the Abbe Limit, it allows new insights into the nano-scaled structure and organization of the chromatin of the nucleus.

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.

In genome analysis, -based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve -mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures.

Inductive intrinsic localized modes in a one-dimensional nonlinear electric transmission line.

The experimental properties of intrinsic localized modes (ILMs) have long been compared with theoretical dynamical lattice models that make use of nonlinear onsite and/or nearest-neighbor intersite potentials. Here it is shown for a one-dimensional lumped electrical transmission line that a nonlinear inductive component in an otherwise linear parallel capacitor lattice makes possible a new kind of ILM outside the plane wave spectrum. To simplify the analysis, the nonlinear inductive current equations are transformed to flux transmission line equations with analog onsite hard potential nonlinearities.

Molecular epidemiology of tuberculosis in Victoria, Australia, reveals low level of transmission.

Setting: Victoria, Australia.

Objective: To measure the level of Mycobacterium tuberculosis transmission in Victoria.

Design: Retrospective analysis of mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing profiles from all first M.

Supertransmission channel for an intrinsic localized mode in a one-dimensional nonlinear physical lattice.

It is well known that a moving intrinsic localized mode (ILM) in a nonlinear physical lattice looses energy because of the resonance between it and the underlying small amplitude plane wave spectrum. By exploring the Fourier transform (FT) properties of the nonlinear force of a running ILM in a driven and damped 1D nonlinear lattice, as described by a 2D wavenumber and frequency map, we quantify the magnitude of the resonance where the small amplitude normal mode dispersion curve and the FT amplitude components of the ILM intersect. We show that for a traveling ILM characterized by a specific frequency and wavenumber, either inside or outside the plane wave spectrum, and for situations where both onsite and intersite nonlinearity occur, either of the hard or soft type, the strength of this resonance depends on the specific mix of the two nonlinearities.