Biophysics Reports

2021 Vol. 7, No. 1

Cover Story

Tumour vasculature is known to be aberrant, tortuous and erratic which can have significant implications for fluid flow. Fluid dynamics in tumour tissue plays an important part in tumour growth, metastasis and the delivery of therapeutics. Mathematical models are increasingly employed to elucidate the complex interplay between various aspects of the tumour vasculature and fluid flow. Previous models usually assume a uniformly distributed vasculature without explicitly describing its architecture or incorporate the distribution of vasculature without accounting for real geometric features of the network. In this study, an integrated computational model is developed by resolving fluid flow at the single capillary level across the whole tumour vascular network. It consists of an angiogenesis model and a fluid flow model which resolves flow as a function of the explicit vasculature by coupling intravascular flow and interstitial flow in tumour tissue. The integrated model has been used to examine the influence of microvascular distribution, necrosis and vessel pruning on fluid flow, as well as the effect of heterogeneous vessel permeability. The results reveal the level of nonuniformity in tumour interstitial fluid pressure (IFP), with large variations in IFP profile between necrotic and non-necrotic tumours. Changes in microscopic features of the vascular network can significantly influence fluid flow in the tumour where removal of vessel blind ends has been found to reduce IFP and promote interstitial fluid flow. The results demonstrate the importance of incorporating microscopic properties of the tumour vasculature and intravascular flow when predicting fluid flow in tumour tissue.

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PROTOCOL

Probing lysosomal activity in vivo

Xin Li, Yanan Sun, Xiaochen Wang

2021, 7(1): 1-7. doi: 10.52601/bpr.2021.200047

Abstract(1579)

PDF(110)

Abstract:
Lysosomes are membrane-bound organelles for biomolecule degradation and recycling. They also serve as a nutrient sensing and signaling center to maintain cell and tissue homeostasis. Lysosomal properties alter in response to developmental or environmental cues, but these changes are hard to track in vivo. Employing C. elegans as a model system, we have developed assays to examine and quantify lysosome properties in vivo, including lysosome maturation, acidification and cleavage activity. These assays can be used to reveal alterations of lysosomal activity during C. elegans development and in stress conditions.

REVIEW

Nanozymes with bioorthogonal reaction for intelligence nanorobots

Si Sun, Xinzhu Chen, Jing Chen, Junying Wang, Xiao-dong Zhang

2021, 7(1): 8-20. doi: 10.52601/bpr.2021.200044

Abstract(1344)

PDF(87)

Abstract:
Bioorthogonal reactions have attained great interest and achievements in various fields since its first appearance in 2003. Compared to traditional chemical reactions, bioorthogonal chemical reactions mediated by transition metals catalysts can occur under physiological conditions in the living system without interfering with or damaging other biochemical events happening simultaneously. The idea of using nanomachines to perform precise and specific tasks in living systems is regarded as the frontier in nanomedicine. Bioorthogonal chemical reactions and nanozymes have provided new potential and strategies for nanomachines used in biomedical fields such as drug release, imaging, and bioengineering. Nanomachines, also called as intelligence nanorobots, based on nanozymes with bioorthogonal reactions show better biocompatibility and water solubility in living systems and perform controlled and adjustable stimuli-triggered response regarding to different physiological environments. In this review, we review the definition and development of bioorthogonal chemical reactions and describe the basic principle of bioorthogonal nanozymes fabrication. We also review several controlled and adjustable stimuli-triggered intelligence nanorobots and their potential in therapeutic and engineered applications. Furthermore, we summarize the challenges in the use of intelligence nanorobots based on nanozymes with bioorthogonal chemical reactions and propose promising vision in smart nanodevices along this appealing avenue of research.

Structurally reconfigurable designer RNA structures for nanomachines

Kai Jiao, Yaya Hao, Fei Wang, Lihua Wang, Chunhai Fan, Jiang Li

2021, 7(1): 21-34. doi: 10.52601/bpr.2021.200053

Abstract(1204)

PDF(70)

Abstract:
Structurally reconfigurable RNA structures enable dynamic transitions of the functional states in response to diverse molecular stimuli, which are fundamental in genetic and epigenetic regulations. Inspired by nature, rationally designed RNA structures with responsively reconfigurable motifs have been developed to serve as switchable components for building engineered nanomachines, which hold promise in synthetic biological applications. In this review, we summarize recent progress in the design, synthesis, and integration of engineered reconfigurable RNA structures for nanomachines. We highlight recent examples of their targeted applications such as biocomputing and smart theranostics. We also discuss their advantages, challenges as well as possible solutions. We further provide an outlook of their potential in future synthetic biology.

RESEARCH ARTICLE

The influence of tumour vasculature on fluid flow in solid tumours: a mathematical modelling study

Moath Alamer, Xiao Yun Xu

2021, 7(1): 35-54. doi: 10.52601/bpr.2021.200041

Abstract(976)

PDF(68)

Abstract:
Tumour vasculature is known to be aberrant, tortuous and erratic which can have significant implications for fluid flow. Fluid dynamics in tumour tissue plays an important part in tumour growth, metastasis and the delivery of therapeutics. Mathematical models are increasingly employed to elucidate the complex interplay between various aspects of the tumour vasculature and fluid flow. Previous models usually assume a uniformly distributed vasculature without explicitly describing its architecture or incorporate the distribution of vasculature without accounting for real geometric features of the network. In this study, an integrated computational model is developed by resolving fluid flow at the single capillary level across the whole tumour vascular network. It consists of an angiogenesis model and a fluid flow model which resolves flow as a function of the explicit vasculature by coupling intravascular flow and interstitial flow in tumour tissue. The integrated model has been used to examine the influence of microvascular distribution, necrosis and vessel pruning on fluid flow, as well as the effect of heterogeneous vessel permeability. Our results reveal the level of nonuniformity in tumour interstitial fluid pressure (IFP), with large variations in IFP profile between necrotic and non-necrotic tumours. Changes in microscopic features of the vascular network can significantly influence fluid flow in the tumour where removal of vessel blind ends has been found to reduce IFP and promote interstitial fluid flow. Our results demonstrate the importance of incorporating microscopic properties of the tumour vasculature and intravascular flow when predicting fluid flow in tumour tissue.

A quantitative method to assess bacterial adhesion using recombinant bioluminescent Pseudomonas aeruginosa

Lu Wang, Xinhua Qiao, Lei Gao, Chang Chen, Yi Wan

2021, 7(1): 55-70. doi: 10.52601/bpr.2021.200043

Abstract(1211)

PDF(48)

Abstract:
Bioluminescence technology has been widely used in the field of medical detection. The bioluminescent lux reporter system provides a non-invasive platform to monitor bacterial growth and expression in real time. This study aimed to establish a method for detecting bacterial adhesion on the surface of materials, including medical devices, by using recombinant bioluminescent Pseudomonas aeruginosa containing a lux reporter. By monitoring the growth and bioluminescent properties of the recombinant PAO1-lux strain, the optimal test conditions for bacterial adhesion detection in vitro were determined to be as follows: an initial inoculation density of 10⁵ to 10⁶ CFU/mL, M9 medium at a pH 6.2, an adhesion time of 6 h, and the collection of adherent bacteria by ultrasonic cleaning. The traditional CFU counting method and the bioluminescence method were compared, and the applicability of the new method was verified by testing the adhesion of bacteria on the surface of various materials. The validated bioluminescent strains could serve as strong candidates to be used as bacterial detection tools in applications such as bacterial adhesion evaluation as well as supplements and alternatives to traditional microbiological testing procedures. In addition, this method has the potential to enable the study of bacterial adhesion on the surface of inanimate objects and living tissues. With the development of this method and its wide applicability, it is expected to become a standard method for the detection of bacterial adhesion and the screening of anti-adhesion materials.

Study on the spatial distribution patterns of histone modifications in Hippo pathway genes

Wenxia Su, Dimeng Zhang, Qiang Zhang, Qianzhong Li

2021, 7(1): 71-79. doi: 10.52601/bpr.2021.200042

Abstract(697)

PDF(34)

Abstract:
Hippo pathway can regulate cell division, differentiation and apoptosis, and control the shape and size of organs. To study the distribution patterns of histone modifications of Hippo pathway genes in embryonic stem cells is helpful to understand the molecular regulation mechanism of histone modification and Hippo pathway on stem cell self-renewal. In this study, 19 genes of Hippo pathway including YAP, TAZ, LATS1/2, MST1 and SAV1, and eight histone modifications in embryonic stem cells were chosen to study the spatial distribution patterns of histone modifications. It was found that there were obvious type specificity and the location preference of target regions in the distributions of histone modifications, and H3K4me3 and H3K36me3 played the most important regulatory roles. Through the correlation analysis of histone modifications, a histone modification functional cluster composed of H3K4ac, H3K4me3, H3K9ac and H3K27ac was detected in YAP. In addition, the spatial distribution patterns of histone modifications in Hippo pathway genes were obtained, which provided a new theoretical reference for elucidating the mechanism of histone modifications regulating the gene expression of Hippo pathway, and for revealing the molecular regulatory mechanism of histone modifications affecting the self-renewal of embryonic stem cells by regulating the Hippo pathway.