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Paper microfluidics has attracted much attention since its first introduction around one decade ago due to the merits such as low cost, ease of fabrication and operation, portability, and facile integration with other devices. The dominant application for paper microfluidics still lies in point-of-care testing (POCT), which holds great promise to provide diagnostic tools to meet the ASSURED criteria. With micro/nanostructures inside, paper substrates provide a natural 3D scaffold to mimic native cellular microenvironments and create excellent biointerfaces for cell analysis applications, such as long-term 3D cell culture, cell capture/phenotyping, and cell-related biochemical analysis (small molecules, protein DNA, etc.). This review summarizes cell-related applications based on various engineered paper microdevices and provides some perspectives for paper microfluidics-based cell analysis., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Spatial transcriptomics measures in situ gene expression at millions of locations within a tissue 1 , hitherto with some trade-off between transcriptome depth, spatial resolution and sample size 2 . Although integration of image-based segmentation has enabled impactful work in this context, it is limited by imaging quality and tissue heterogeneity. By contrast, recent array-based technologies offer the ability to measure the entire transcriptome at subcellular resolution across large samples 3-6 . Presently, there exist no approaches for cell type identification that directly leverage this information to annotate individual cells. Here we propose a multiscale approach to automatically classify cell types at this subcellular level, using both transcriptomic information and spatial context. We showcase this on both targeted and whole-transcriptome spatial platforms, improving cell classification and morphology for human kidney tissue and pinpointing individual sparsely distributed renal mouse immune cells without reliance on image data. By integrating these predictions into a topological pipeline based on multiparameter persistent homology 7-9 , we identify cell spatial relationships characteristic of a mouse model of lupus nephritis, which we validate experimentally by immunofluorescence. The proposed framework readily generalizes to new platforms, providing a comprehensive pipeline bridging different levels of biological organization from genes through to tissues., (© 2024. The Author(s).)

Chemical mutagenesis in animal cells is a complex process. Whereas some chemicals are mutagenic in their original form, others such as the nitrosamines and polycyclic hydrocarbon carcinogens are mutagenic only when enzymatically activated. The active form, or ultimate carcinogen, can interact with proteins and nucleic acids, altering amino acids and producing modified bases in DNA. The modified bases do not usually constitute mutations as produced. Instead they are acted on by the DNA enzymes of the cell, which repair most damaged bases but occasionally insert incorrect base sequences at or near the sites of damage. The frequency at which mutant animal cells are recovered depends upon the selection conditions in culture, upon whether the mutation selected is in a gene present in single or multiple active copies, and upon whether expression is dominant or recessive. Many studies depend on selecting for 8-azaguanine- or 6-thioguanine-resistant mutants, which are due to mutations in the HGPRT locus present in a single active copy on the X-chromosome. Other widely used systems depend on selecting for ouabain resistance, which is dominant and results from a change in the sodium/potassium ATPase activity, or on selecting for thymidine kinase mutants in heterozygous Tk+/Tk- mouse cells. Many other types of mutation including nutritional markers are recessive and express only in cells carrying a single active gene copy, as is sometimes the case in established cell lines. The types of base damage causing mutations have been identified in very few cases only, and little is known about the enzymatic mechanisms of mutagenesis. However, chemical mutagenesis in cultured animal cells provide a practical way of testing chemicals and radiations for mutagenicity directly in animal cells, and much has been learned about the mutagenicity of various carcinogenic substances. To date, there is reasonable qualitative agreement between these results and those obtained in the widely used liver microsome-activated bacterial mutagenesis test systems.

Abstract: Circulating hemocytes from larval stages of the paper wasp Polistes dominulus were characterized by light and transmission electron microscopy. Three types were identified: prohemocytes, plasmatocytes and granulocytes. The first two are agranular cells while the latter present typical cytoplasmic inclusions called granules. Plasmatocytes differ from prohemocytes being larger, showing lower nucleus/cytoplasm ratio and they possess many phagolysosomes. The substantial uniformity of most subcellular features and the presence of “intermediate forms” support the “single-cell theory” i.e., there is only one cell line that originates from the prohemocyte and leads to the granular cell passing through the plasmatocyte. This hypothesis seems to be confirmed by functional tests. Indeed, most part of cells adheres to the glass and is able to phagocytize fluorescent microspheres. [Copyright &y& Elsevier]

The natural world provides many examples of multiphase transport and reaction processes that have been optimized by evolution. These phenomena take place at multiple length and time scales and typically include gas-liquid-solid interfaces and capillary phenomena in porous media 1,2 . Many biological and living systems have evolved to optimize fluidic transport. However, living things are exceptionally complex and very difficult to replicate 3-5 , and human-made microfluidic devices (which are typically planar and enclosed) are highly limited for multiphase process engineering 6-8 . Here we introduce the concept of cellular fluidics: a platform of unit-cell-based, three-dimensional structures-enabled by emerging 3D printing methods 9,10 -for the deterministic control of multiphase flow, transport and reaction processes. We show that flow in these structures can be 'programmed' through architected design of cell type, size and relative density. We demonstrate gas-liquid transport processes such as transpiration and absorption, using evaporative cooling and CO 2 capture as examples. We design and demonstrate preferential liquid and gas transport pathways in three-dimensional cellular fluidic devices with capillary-driven and actively pumped liquid flow, and present examples of selective metallization of pre-programmed patterns. Our results show that the design and fabrication of architected cellular materials, coupled with analytical and numerical predictions of steady-state and dynamic behaviour of multiphase interfaces, provide deterministic control of fluidic transport in three dimensions. Cellular fluidics may transform the design space for spatial and temporal control of multiphase transport and reaction processes.

The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.

Bouteloua gracilis (blue grama grass) is one of the most drought and grazing tolerant plants in the short-grass ecosystem. To obtain information on their photosystem activities, we measured the fast (< 1 s) chlorophyll a fluorescence transient (the OJIP curve) from their leaves, and isolated cells grown photoautotrophically in suspension in a culture medium, or with added sucrose. One of our goals was to study the effect of different sucrose concentrations (0, 0.15, 0.3, and 3%) on PSII activity in isolated cells. Our results on cells suspended in culture medium, using the JIP-test, showed a decrease in PSII activity at increasing sucrose concentrations, while the photoautotrophic cells showed an optimal PSII activity, close to that of the leaves. Further, our data on cells grown in 0, 0.15, and 0.3% sucrose, but with added CO2, and measured while the cells were deposited on filter paper, indicate that supplementary CO2 can increase the PSII activity in the presence of sucrose, although further research is necessary to understand these results. [ABSTRACT FROM AUTHOR]

In this issue we highlight three recent papers that demonstrate new strategies to extend the capabilities of paper microfluidics. Paper (a mesh of porous fibers) has a long history as a substrate to perform biomolecular assays. Traditional lateral flow immunoassays (LFAs) are widely used for rapid diagnostic tests, and perform well when a yes or no answer is required and the analyte of interest is at relatively high concentrations. High concentrations are required because usually only a small volume of analyte-containing fluid flows past the detection region, leading to a limited signal. Further, the small pores within paper matrices prevent the use of paper to control the flow of larger particles and cells, limiting the use of paper microfluidics for cell-based diagnostics. The work we highlight addresses these important unmet challenges in paper microfluidics: enriching low concentration analytes to a higher concentration in a smaller volume that can be processed effectively, and using paper to pump flows in larger channels amenable to cells. Applying these new approaches may allow diagnosis of disease states currently technically unachievable using current LFA systems, while maintaining many of the “un-instrumented” advantages of an assay on self-wicking paper. [ABSTRACT FROM AUTHOR]

How cells adopt different identities has long fascinated biologists. Signal transduction in response to environmental cues results in the activation of transcription factors that determine the gene-expression program characteristic of each cell type. Technological advances in the study of 3D chromatin folding are bringing the role of genome conformation in transcriptional regulation to the fore. Characterizing this role of genome architecture has profound implications, not only for differentiation and development but also for diseases including developmental malformations and cancer. Here we review recent studies indicating that the interplay between transcription and genome conformation is a driving force for cell-fate decisions.

Abstract: During past decades, the considerable efforts have been made to utilize lignocellulose as biomass feedstock for the optimal production of bio-ethanol as an alternative source of fuel. In this work, the effective bioconversion of paper sludge to ethanol was investigated by using Zymomonas mobilis NBRC 13756. Major components of the raw paper sludge were carbohydrates and ash. Fermentation utilizing strains of Z. mobilis instead of traditional yeasts and the use of simultaneous saccharification and fermentation (SSF) process have been proposed due to their high ethanol yields with cost-effectiveness. Free cells of Z. mobilis resulted in no ethanol production even after 24h of incubation because cells’ growth was inhibited by metal ions contained in the paper sludge. The application of SSF with Ca-alginate-immobilized cells of Z. mobilis was performed and 18g/L of ethanol was obtained after 48h of incubation at an initial paper sludge concentration of 200g/L. In addition, the repeated batch fermentation of Ca-alginate-immobilized Z. mobilis cells was attempted for producing ethanol up to run 4. Our work suggests that Ca-alginate-immobilized cells of Z. mobilis could effectively produce ethanol from paper sludge not only under the batch fermentation but also under the repeated batch fermentation. [Copyright &y& Elsevier]

The aim of this study was to develop a PCR-based rapid method to detect Bacillus cereus group cells from paper and cardboard. Primers targeting the 16S rDNA and real-time PCR with SYBR green I detection were used in order to be able to also quantify the target. Both autoclaved cardboard samples spiked with B. cereus vegetative cells or spores and naturally contaminated paper and cardboard samples were studied. Results were compared with culturing verified by commercial (API) tests. Several different methods were tested for DNA isolation from the paper and cardboard samples. Two commercial kits intended for soils, the UltraClean soil DNA kit and the FastDNA spin kit for soil, gave the most reproducible results. In spiked samples, the average yield was 50% of added vegetative cells, but spore yield was only about 10%. PCR results from adding vegetative cells correlated with added colony-forming unit (cfu) values (r=0.93, P <0.001) in the range 100–10,000 cfu g-1. Three out of nine studied paper and cardboard samples contained B. cereus group bacteria, based both on culturing and real-time PCR. The numbers were 102–103 bacteria g-1; and PCR gave somewhat higher results than culturing. Thus, real-time PCR can be used as a rapid semi-quantitative method to screen paper and cardboard samples for contamination with B. cereus group bacteria. [ABSTRACT FROM AUTHOR]

Single cells in genetically homogeneous microbial cultures exhibit marked phenotypic heterogeneity that is considered to bolster the fitness of the whole population. Heterogeneity on the single-cell level is typically masked in conventional studies of microbial populations, which rely on data averaged across thousands or millions of cells in a sample. Here we introduce confocal Raman microspectroscopy as a method for investigating and illustrating the spatial heterogeneity of microbial cell populations. By the use of three different test organisms as model systems, we show pronounced cellular heterogeneity even in colonies cultivated under laboratory conditions. [ABSTRACT FROM AUTHOR]

Abstract: Different histochemical techniques were applied to examine the morphological features of the secretory cells of hypopharyngeal glands in the wasp Polistes versicolor. The results showed that most analyzed individuals present active glands with secretion stored in the cytoplasm. In some glands, morphological analyses revealed the presence of degenerative characteristics. Analyses of cellular integrity, however, did not detect dead cells. The results showed that, in P. versicolor, the development and regression of the hypopharyngeal glands were not age related, unlike glands of social bees. [Copyright &y& Elsevier]

Prolonged quiescence of haematopoietic stem cells has been proposed to support durable haematopoiesis through clonal succession. Genetic experiments in mice have implicated the cyclin-dependent kinase inhibitor (cdki) p21Waf1 in sustaining stem cell quiescence, and the cdki p27Kip1 in inhibiting the expansion of more mature progenitor cells. The expression of these inhibitory proteins in human haematopoietic stem cell candidates has not hitherto been studied. We describe a rare subpopulation (3 × 10−7 umbilical cord mononuclear cells) of lineage-negative cells that exhibited sustained resistance over months to cytokine-induced cycling, and characterized the expression of p21Waf1 and p27Kip1 proteins in these cells. Whereas p27Kip1 was uniformly expressed in these cells, the expression of p21Waf1 in this population and in lineage-negative CD34+ cells was variable. For this rare subset of cells exhibiting prolonged quiescence, p21Waf1 may be dispensable and p27Kip1 necessary for growth arrest. [ABSTRACT FROM AUTHOR]

This article presents various studies related to women's health, as of September 1, 2003. According to a study as a consequence of mammographic breast screening programmes, ductal carcinoma in situ is diagnosed with increasing frequency. Mastectomy for localised ductal carcinoma in situ is thought to be an over-treatment by many physicians, but there is much controversy as to whether complete local excision alone is sufficient. Another study was undertaken to compare postcolposcopy management strategies for women referred for low-grade squamous intraepithelial lesions or oncogenic human a papillomavirus DNA-positive atypical squamous cells of undetermined significance, with cervical intraepithelial neoplasia grade 1 or less found at initial colposcopy. A study was also undertaken to compare alternative strategies for the initial management of a cytologic diagnosis of atypical squamous cells of undetermined significance.

Heterotrimeric G-proteins transduce signals from heptahelical transmembrane receptors to different effector systems, regulating diverse complex intracellular pathways and functions. In brain, facilitation of depolarization-induced neurotransmitter release for synaptic transmission is mediated by Gsα and Gqα. To identify effectors for Gα-proteins, we performed a yeast two-hybrid screening of a human brain cDNA library, using the human Gαs protein as a bait. We identified a protein member of the synembryn family as one of the interacting proteins. Extending the study to other Gα subunits, we found that Gqα also interacts with synembryn, and these interactions were confirmed by in vitro pull down studies and by in vivo confocal laser microscopy analysis. Furthermore, synembryn was shown to translocate to the plasma membrane in response to carbachol and isoproterenol. This study supports recent findings in C. elegans where, through genetic studies, synembryn was shown to act together with Gqα regulating neuronal transmitter release. Based on these observations, we propose that synembryn is playing a similar role in human neuronal cells. © 2003 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Simple Summary: The paper describes the statistical analysis of the response of gastric cancer cells and normal cells to broadband terahertz radiation up to 4 THz, both with and without the use of nanostructured contrast agents. A statistical analysis was conducted towards multiple pairwise comparisons in order to identify the narrow THz frequency ranges where the contrast is enhanced and allows a clear identification of tumor cells in the presence of contrast agents. The paper describes the statistical analysis of the response of gastric cancer cells and normal cells to broadband terahertz radiation up to 4 THz, both with and without the use of nanostructured contrast agents. The THz spectroscopy analysis was comparatively performed under the ATR procedure and transmission measurement procedure. The statistical analysis was conducted towards multiple pairwise comparisons, including a support medium (without cells) versus a support medium with nanoparticles, normal cells versus normal cells with nanoparticles, and, respectively, tumor cells versus tumor cells with nanoparticles. When generally comparing the ATR procedure and transmission measurement procedure for a broader frequency domain, the differentiation between normal and tumor cells in the presence of contrast agents is superior when using the ATR procedure. THz contrast enhancement by using contrast agents derived from MRI-related contrast agents leads to only limited benefits and only for narrow THz frequency ranges, a disadvantage for THz medical imaging. [ABSTRACT FROM AUTHOR]

This paper explores a formal model of autopoiesis as presented by Maturana, Uribe and Varela, and analyzes this model and its implications through the lens of the notions of eigenforms (fixed points) and the intricacies of Goedelian coding. The paper discusses the connection between autopoiesis and eigenforms and a variety of different perspectives and examples. The paper puts forward original philosophical reflections and generalizations about its various conclusions concerning specific examples, with the aim of contributing to a unified way of understanding (formal models of) living systems within the context of natural sciences, and to see the role of such systems and the formation of information from the point of view of analogs of biological construction. To this end, we pay attention to models for fixed points, self-reference and self-replication in formal systems and in the description of biological systems. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, the numerical treatment for two nonlinear advance delay differential system is discussed. This system arises during the study of conduction of impulses down myelinated axons, incorporating electrical properties of the myelin. This system consists of two coupled first-order equations, one having a delay term and the other having an advance one. The modified difference scheme is used and then applied to some test problems. [Copyright &y& Elsevier]

Describes an expressed sequence tag analysis of skin cells of Japanese flounder Paralichthys olivaceus. Isolation of messenger RNA of skin; Conversion of phage clones into plasmids; Average sequence length.

This article presents information on a gradient of bicoid (bcd) protein in drosophila embryos. According to the concept of positional information, the concentration of a morphogen instructs cells within an embryonic field of their position. The cells then interpret this information by an appropriate program of differentiation. Several models have been proposed that describe the generation of stable gradients of morphogens which could specify subregions of the embryo in a concentration-dependent manner.

Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage., (© 2024. The Author(s).)

In the current paper we provide a proof of NP-completeness for the Cell Formation Problem (CFP) with the fractional grouping efficacy objective function. First the CFP with a linear objective function is considered. Following the ideas of Pinheiro et al. (2016) we show that it is equivalent to the Bicluster Graph Editing Problem (BGEP), which is known to be NP-complete due to the reduction from the 3-Exact 3-Cover Problem – 3E3CP (Amit, 2004). Then we suggest a polynomial reduction of the CFP with the linear objective to the CFP with the grouping efficacy objective. It proves the NP-completeness of this fractional CFP formulation. Along with the NP-status our paper presents important connections of the CFP with the BGEP and 3E3CP. Such connections could be used for "transferring" of known theoretical properties, efficient algorithms, polynomial cases, and other features of well-studied graph editing and exact covering problems to the CFP. [ABSTRACT FROM AUTHOR]

The blood-brain barrier (BBB) protects the brain by actively allowing the entry of ions and nutrients while limiting the passage of from toxins and pathogens. A healthy BBB has low permeability and high selectivity to maintain normal brain functions. Increased BBB permeability can result from neurological diseases and traumatic injuries. Modern engineering technologies such as microfluidics and fabrication techniques have advanced the development of BBB models to simulate the basic functions of BBB. However, the intrinsic BBB properties are difficult to replicate. Existing in vitro BBB models demonstrate inconsistent BBB permeability and selectivity due to variations in microfluidic design, cell types and arrangement, expression of tight junction (TJ) proteins, and use of shear stress. Specifically, microfluidic designs have flow channels of different sizes, complexity, topology, and modular structure. Different cell types are selected to mimic various physiological conditions. These factors make it challenging to compare results obtained using different experimental setups. This paper highlights key factors that play important roles in influencing microfluidic models and discusses how these factors contribute to permeability and selectivity of the BBB models. [ABSTRACT FROM AUTHOR]

We have shown previously that the processing of asparagine-linked oligosaccharides in baby hamster kidney (BHK) cells is blocked only partially by the glucosidase inhibitors, 1-deoxynojidmycin and A'-methyl-1-deoxynojidmycin [Hughes, R, C, Foddy, L. & Bause, E. (1987) Biochem. J. 247, 537-544], Similar results are now reported for castanospermine, another inhibitor of processing glucosidases, and a detailed study of oligosaccharide processing in the inhibited cells is reported. In steady-state conditions the major endo-H-released oligosaccharides contained glucose residues but non-glycosylated oligosaccharides, including Man9GlcNAc to Man5GlcNAc, were also present. To determine the processing sequences occurring in the presence of castanospermine, BHK cells were pulse-labelled for various times with [³H]mannose and the oligosaccharide intermediates, isolated by gel filtration and paper chromatography, characterized by acetolysis and sensitivity to jack bean α-mannosidase. The data show that Glc3Man8GlcNAc2 is transferred to protein and undergoes processing to produce Glc3Man8GlcNAc2 and Glc3Man7GlcNAc2 as major species as well as a smaller amount of Man9GlcNAc2, Glucosidase-processed intermediates, Glc1Man8GlcNAc2 and Glc1Man7GlcNAc2, were also obtained as well as a Man7GlcNAc2 species derived from Glc1Man7GlcNAc2 and different from the Man7GlcNAc2 isomer formed in the usual processing pathway. No evidence for the direct transfer of non-glucosylated oligosacchaddes to proteins was obtained and we conclude that the continued assembly of complex-type glycans in castanospermine-inhibited BHK cells results from residual activity of processing glucosidases. [ABSTRACT FROM AUTHOR]