Biology Of System Research Articles

Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems

BackgroundThe Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems.ResultsBiSDL’s effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers.ConclusionsBiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.

Analysis of Student Learning Outcomes on Biology of The Blood Circulation System in Senior High School

The importance of analyzing the learning process becomes a very significant impetus when it is considered a process of changing student behavior. Evaluation is the process of collecting, assessing, and interpreting data to ensure the level of achievement of a student's learning goals. This study aims to determine student learning outcomes on circulatory system biology material class XI Senior High School. The method used in this study is the quantitative descriptive method. The result of this study is that the average score obtained by students after doing the question is 30.54 with the highest score of 56 points and the lowest score of 12 points. Of the 11 students who did 25 test questions, three students with the highest rankings and three students with the lowest rankings were obtained. Based on the results of research that has been carried out, it can be concluded that students have a good interest in learning the material of the circulatory system. However, some students are still unable to understand the material due to the lack of precise selection of learning methods and media applied by teachers in the learning process.

Insights into the inhibition of protospacer integration via direct interaction between Cas2 and AcrVA5.

Spacer acquisition step in CRISPR-Cas system involves the recognition and subsequent integration of protospacer by the Cas1-Cas2 complex in CRISPR-Cas systems. Here we report an anti-CRISPR protein, AcrVA5, and reveal the mechanisms by which it strongly inhibits protospacer integration. Our biochemical data shows that the integration by Cas1-Cas2 was abrogated in the presence of AcrVA5. AcrVA5 exhibits low binding affinity towards Cas2 and acetylates Cas2 at Lys55 on the binding interface of the Cas2 and AcrVA5 N-terminal peptide complex to inhibit the Cas2-mediated endonuclease activity. Moreover, a detailed structural comparison between our crystal structure and homolog structure shows that binding of AcrVA5 to Cas2 causes steric hindrance to the neighboring protospacer resulting in the partial disassembly of the Cas1-Cas2 and protospacer complex, as demonstrated by electrophoretic mobility shift assay. Our study focuses on this mechanism of spacer acquisition inhibition and provides insights into the biology of CRISPR-Cas systems.

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.

Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.

Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins.

Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology. We have recently demonstrated the success of an anaerobic single-particle cryoEM workflow applied to the air-sensitive nitrogenase enzymes. In this protocol, we detail the use of Schlenk lines and anaerobic chambers to prepare samples, including a protein tag for monitoring sample exposure to oxygen in air. We describe how to use a plunge freezing apparatus inside of a soft-sided vinyl chamber of the type we routinely use for anaerobic biochemistry and crystallography of oxygen-sensitive proteins. Manual control of the airlock allows for introduction of liquid cryogens into the tent. A custom vacuum port provides slow, continuous evacuation of the tent atmosphere to avoid accumulation of flammable vapors within the enclosed chamber. These methods allowed us to obtain high-resolution structures of both nitrogenase proteins using single-particle cryoEM. The procedures involved can be generally subdivided into a 4 d anaerobic sample generation procedure, and a 1 d anaerobic cryoEM sample preparation step, followed by conventional cryoEM imaging and processing steps. As nitrogen is a substrate for nitrogenase, the Schlenk lines and anaerobic chambers described in this procedure are operated under an argon atmosphere; however, the system and these procedures are compatible with other controlled gas environments.

Student metacognition in online learning using website hyperlink facilities on Microsoft Team’s platform

Without the ability to analyze their own learning (metacognition), students can find it difficult to manage their educational journey. The good news is, future learning environments on online platforms offer innovative ways to develop these skills, even for those who are digital natives. This study aims to ascertain the effectiveness of online learning by using a website hyperlink-based teaching and learning scenario, especially using the Microsoft Teams platform towards students’ metacognition during online learning. Both metacognition knowledge and awareness (regulation), representing the metacognition, were checked. Coordination systems in learning biology were the chosen topics to be taught in quasi-experimental research using a pretest-posttest nonequivalent control group design. Two classes were selected purposely based on the normality and homogeneity test to have the controlled and experimental classes. We examined the metacognitive knowledge and awareness using tests and questionnaires. We checked the effectiveness of the web hyperlink-based media on students’ metacognition knowledge and awareness using MANOVA Regression analysis and N-Gain scores. Our developed web hyperlink-based media has significantly enhanced students’ cognitive knowledge and awareness.

Chemical Organization Theory as a General Modeling Framework for Self-Sustaining Systems

This paper summarizes and reviews Chemical Organization Theory (COT), a formalism for the analysis of complex, self-organizing systems across multiple disciplines. Its elements are resources and reactions. A reaction maps a set of resources onto another set, thus representing an elementary process that transforms resources into new resources. Reaction networks self-organize into invariant subnetworks, called ‘organizations’, which are attractors of their dynamics. These are characterized by closure (no new resources are added) and self-maintenance (no existing resources are lost). Thus, they provide a simple model of autopoiesis: the organization persistently recreates its own components. The resilience of organizations in the face of perturbations depends on properties such as the size of their basin of attraction and the redundancy of their reaction pathways. Application domains of COT include the origin of life, systems biology, cognition, ecology, Gaia theory, sustainability, consciousness, and social systems.

An open-source FACS automation system for high-throughput cell biology.

Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instrument's software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology.

CSIM: A Fast Community Detection Algorithm Based on Structure Information Maximization

Community detection has been a subject of extensive research due to its broad applications across social media, computer science, biology, and complex systems. Modularity stands out as a predominant metric guiding community detection, with numerous algorithms aimed at maximizing modularity. However, modularity encounters a resolution limit problem when identifying small community structures. To tackle this challenge, this paper presents a novel approach by defining community structure information from the perspective of encoding edge information. This pioneering definition lays the foundation for the proposed fast community detection algorithm CSIM, boasting an average time complexity of only O(nlogn). Experimental results showcase that communities identified via the CSIM algorithm across various graph data types closely resemble ground truth community structures compared to those revealed via modularity-based algorithms. Furthermore, CSIM not only boasts lower time complexity than greedy algorithms optimizing community structure information but also achieves superior optimization results. Notably, in cyclic network graphs, CSIM surpasses modularity-based algorithms in effectively addressing the resolution limit problem.

Artificial Intelligence in Biology

This article provides an in-depth analysis of the use of Artificial Intelligence (AI) in various aspects of biology, including healthcare, agriculture, and environmental monitoring. It highlights AI's ability to mimic human intelligence and analyze large datasets for predictions and tasks. The article also discusses its integration into Chinese medicine, where AI-guided diagnostic and therapeutic systems optimize clinical treatments and health management. AI is also used in disease management, analyzing data on diseases and pests, predicting their impact on ecosystems, and implementing preventative measures. The article also highlights the role of integrated information systems in environmental monitoring. Artificial intelligence (AI) has significant potential in healthcare research and chemical discoveries. Pharmaceutical companies are using AI to improve drug development by utilizing computational biology and machine learning systems to predict molecular behavior and the likelihood of finding a useful drug. This saves time and money on unnecessary tests. Clinical studies, electronic medical records, high-resolution medical images, and genomic profiles can be used as resources for drug development. Strong AI systems can analyze extensive data sets in pharmaceutical and medical research. This review focuses on integrating knowledge of cancer drugs, drug resistance, next-generation sequencing, genetic variants, and structural biology in cancer precision drug discovery.

Recent developments in the use of nanocrystals to improve bioavailability of APIs.

Nanocrystals refer to materials with at least one dimension smaller than 100 nm, composing of atoms arranged in single crystals or polycrystals. Nanocrystals have significant research value as they offer unique advantages over conventional pharmaceutical formulations, such as high bioavailability, enhanced targeting selectivity and controlled release ability and are therefore suitable for the delivery of a wide range of drugs such as insoluble drugs, antitumor drugs and genetic drugs with broad application prospects. In recent years, research on nanocrystals has been progressively refined and new products have been launched or entered the clinical phase of studies. However, issues such as safety and stability still stand that need to be addressed for further development of nanocrystal formulations, and significant gaps do exist in research in various fields in this pharmaceutical arena. This paper presents a systematic overview of the advanced development of nanocrystals, ranging from the preparation approaches of nanocrystals with which the bioavailability of poorly water-soluble drugs is improved, critical properties of nanocrystals and associated characterization techniques, the recent development of nanocrystals with different administration routes, the advantages and associated limitations of nanocrystal formulations, the mechanisms of physical instability, and the enhanced dissolution performance, to the future perspectives, with a final view to shed more light on the future development of nanocrystals as a means of optimizing the bioavailability of drug candidates. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Magnetic modulation of lysosomes for cancer therapy.

Lysosomes play a central role in biochemical signal transduction and oxidative stress in cells. Inducing lysosome membrane penetration (LMP) to cause lysosomal-dependent cell death (LCD) in tumor cells is an effective strategy for cancer therapy. Chemical drugs can destroy the stability of lysosomes by neutralizing protons within the lysosomes or enhancing the fragility of the lysosomal membranes. However, there remain several unsolved problems of traditional drugs in LMP induction due to insufficient lysosomal targeting, fast metabolism, and toxicity in normal cells. With the development of nanotechnology, magnetic nanoparticles have been demonstrated to target lysosomes naturally, providing a versatile tool for lysosomal modulation. Combined with excellent tissue penetration and spatiotemporal manipulability of magnetic fields, magnetic modulation of lysosomes progresses rapidly in inducing LMP and LCD for cancer therapy. This review comprehensively discussed the strategies of magnetic modulation of lysosomes for cancer therapy. The intrinsic mechanisms of LMP-induced LCD were first introduced. Then, the modulation of lysosomes by diverse physical outputs of magnetic fields was emphatically discussed. Looking forward, this review will shed the light on the prospect of magnetic modulation of lysosomes, inspiring future research of magnetic modulation strategy in cancer therapy. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

New insights into nanomedicines for oral delivery of glucagon-like peptide-1 analogs.

Type 2 diabetes mellitus (T2DM) is a metabolic disorder that arises when the body cannot respond fully to insulin, leading to impaired glucose tolerance. Currently, the treatment embraces non-pharmacological actions (e.g., diet and exercise) co-associated with the administration of antidiabetic drugs. Metformin is the first-line treatment for T2DM; nevertheless, alternative therapeutic strategies involving glucagon-like peptide-1 (GLP-1) analogs have been explored for managing the disease. GLP-1 analogs trigger insulin secretion and suppress glucagon release in a glucose-dependent manner thereby, reducing the risk of hyperglycemia. Additionally, GLP-1 analogs have an extended plasma half-life compared to the endogenous peptide due to their high resistance to degradation by dipeptidyl peptidase-4. However, GLP-1 analogs are mainly administered via subcutaneous route, which can be inconvenient for the patients. Even considering an oral delivery approach, GLP-1 analogs are exposed to the harsh conditions of the gastrointestinal tract (GIT) and the intestinal barriers (mucus and epithelium). Hereupon, there is an unmet need to develop non-invasive oral transmucosal drug delivery strategies, such as the incorporation of GLP-1 analogs into nanoplatforms, to overcome the GIT barriers. Nanotechnology has the potential to shield antidiabetic peptides against the acidic pH and enzymatic activity of the stomach. In addition, the nanoparticles can be coated and/or surface-conjugated with mucodiffusive polymers and target intestinal ligands to improve their transport through the intestinal mucus and epithelium. This review focuses on the main hurdles associated with the oral administration of GLP-1 and GLP-1 analogs, and the nanosystems developed to improve the oral bioavailability of the antidiabetic peptides. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Lymphatic System and the Kidney: From Lymphangiogenesis to Renal Inflammation and Fibrosis Development.

The lymphatic kidney system plays a crucial role in managing interstitial fluid removal, regulating fluid balance, and tuning immune response. It also assists in the reabsorption of proteins, electrolytes, cytokines, growth factors, and immune cells. Pathological conditions, including tissue damage, excessive interstitial fluid, high blood glucose levels, and inflammation, can initiate lymphangiogenesis-the formation of new lymphatic vessels. This process is associated with various kidney diseases, including polycystic kidney disease, hypertension, ultrafiltration challenges, and complications post-organ transplantation. Although lymphangiogenesis has beneficial effects in removing excess fluid and immune cells, it may also contribute to inflammation and fibrosis within the kidneys. In this review, we aim to discuss the biology of the lymphatic system, from its development and function to its response to disease stimuli, with an emphasis on renal pathophysiology. Furthermore, we explore how innovative treatments targeting the lymphatic system could potentially enhance the management of kidney diseases.

An overview of serology and molecular biology of the Rh blood group system

An overview of serology and molecular biology of the Rh blood group system

The landscape of transcription factor promoter activity during vegetative development in Marchantia.

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterising the transcriptional activity of TF genes in space and time is a critical step towards understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analysed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

Alternative Renin-Angiotensin System.

The renin-angiotensin system is the most important peptide hormone system in the regulation of cardiovascular homeostasis. Its classical arm consists of the enzymes, renin, and angiotensin-converting enzyme, generating angiotensin II from angiotensinogen, which activates its AT1 receptor, thereby increasing blood pressure, retaining salt and water, and inducing cardiovascular hypertrophy and fibrosis. However, angiotensin II can also activate a second receptor, the AT2 receptor. Moreover, the removal of the C-terminal phenylalanine from angiotensin II by ACE2 (angiotensin-converting enzyme 2) yields angiotensin-(1-7), and this peptide interacts with its receptor Mas. When the aminoterminal Asp of angiotensin-(1-7) is decarboxylated, alamandine is generated, which activates the Mas-related G-protein-coupled receptor D, MrgD (Mas-related G-protein-coupled receptor type D). Since Mas, MrgD, and the AT2 receptor have opposing effects to the classical AT1 receptor, they and the enzymes and peptides activating them are called the alternative or protective arm of the renin-angiotensin system. This review will cover the historical aspects and the current standing of this recent addition to the biology of the renin-angiotensin system.

The Mediterranean mussel Mytilus galloprovincialis: a novel model for developmental studies in mollusks.

A model organism in developmental biology is defined by its experimental amenability and by resources created for the model system by the scientific community. For the most powerful invertebrate models, the combination of both has already yielded a thorough understanding of developmental processes. However, the number of developmental model systems is still limited, and their phylogenetic distribution heavily biased. Members of one of the largest animal lineages, the Spiralia, for example, have long been neglected. In order to remedy this shortcoming, we have produced a detailed developmental transcriptome for the bivalve mollusk Mytilus galloprovincialis, and have expanded the list of experimental protocols available for this species. Our high-quality transcriptome allowed us to identify transcriptomic signatures of developmental progression and to perform a first comparison with another bivalve mollusk: the Pacific oyster Crassostrea gigas. To allow co-labelling studies, we optimized and combined protocols for immunohistochemistry and hybridization chain reaction to create high-resolution co-expression maps of developmental genes. The resources and protocols described here represent an enormous boost for the establishment of Mytilus galloprovincialis as an alternative model system in developmental biology.

Review of Model Systems in Biology: History, Philosophy, and Practical Concerns by Georg Striedter

Review of <i>Model Systems in Biology: History, Philosophy, and Practical Concerns</i> by Georg Striedter

Selfing in epiphytic bromeliads compensates for the limited pollination services provided by nectarivorous bats in a neotropical montane forest.

Abstract. Plants with specialized pollination systems frequently exhibit adaptations for self-pollination, and this contradictory situation has been explained in terms of the reproductive assurance function of selfing. In the neotropics, several plant lineages rely on specialized vertebrate pollinators for sexual reproduction, including the highly diverse Bromeliaceae family, which also displays a propensity for selfing. Thus far, the scarce evidence on the role of selfing in bromeliads and in other neotropical plant groups is inconclusive. To provide insights into the evolution and persistence of self-fertilization in the breeding systems of Bromeliaceae, we studied four sympatric epiphytic species from the genus Werauhia (Tillandsioideae) in Costa Rica. We documented their floral biology, pollination ecology and breeding systems. We estimated the contribution of selfing by comparing the reproductive success between emasculated flowers requiring pollinator visits and un-manipulated flowers capable of selfing and exposed to open pollination across two flowering seasons. The studied species displayed specialized pollination by nectar-feeding bats as well as a high selfing ability (auto-fertility index values > 0.53), which was attained by a delayed selfing mechanism. Fruit set from natural cross-pollination was low (<26% in both years) and suggested limited pollinator visitation. In line with this, we found a very low bat visitation to flowers using video-camera recording, from 0 to 0.24 visits per plant per night. On the contrary, the contribution of selfing was comparatively significant since 54-80% of the fruit set from un-manipulated flowers can be attributed to autonomous self-pollination. We concluded that inadequate cross-pollination services diminished the reproductive success of the studied Werauhia, which was compensated for by a delayed selfing mechanism. The low negative effects of inbreeding on seed set and germination likely reinforce the persistence of selfing in this bromeliad group. These results suggest that selfing in bat-pollinated bromeliads may have evolved as a response to pollinator limitation.