Complex Organisms Research Articles

Extensive Oceanic Anoxia during the early Cambrian: Evidence from Mn-Carbonate and Alabandite Deposition in the Northwestern Yangtze margin, South China

The Cambrian Explosion, which is characterized by complex organisms radiation after ~521 Ma, has led to speculation about low levels of ocean oxygenation during the Early Cambrian (~541–521 Ma). Recently, the genesis of sedimentary Mn-deposits has provided a new perspective for understanding the redox status of ancient oceans. The present study reevaluates the redox conditions of the Early Cambrian Ocean in South China using sedimentary records of Mn-deposits. The Mn-deposits developed in the Lower Cambrian Qiujiahe Formation on the northwestern Yangtze margin, covering slope/basin-to-shelf environments. The combined sedimentological, mineralogical, and geochemical evidence indicates that Mn-deposits lack of Mn-oxide precursors and exhibited hydrothermal-type REE patterns and δ13C distributions. Mn‑carbonates and partially alabandite (MnS) were directly precipitated in Mn-rich anoxic waters. The Mn-bearing rocks exhibited high total organic matter content (TOC, average 3.96 %), and pyrite layers developed, indicating active anaerobic sulfate reduction with the removal of Fe before Mn-deposition. The increased of the pH and sulfurization degree, promoting the Mn-minerals precipitation in water columns. The widespread Mn deposition across slope/basin-to-shelf areas represents the sedimentary response to the extensive ocean anoxia during the Early Cambrian. Such a scenario aids in elucidating the evolution of early life, suggesting that extensive ocean anoxia likely contributed to delaying the radiation of complex animals during the Cambrian Explosion.

START domains generate paralog-specific regulons from a single network architecture.

Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB ( ~ 99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered 'responsive' versus 'non-responsive' by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.

A multicellular developmental program in a close animal relative.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes1,2. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii-a close relative that diverged from animals about 1 billion years ago3,4-undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

Comprehensive Exploration of CRISPR and Gene Editing Technologies: Applications, Ethical Considerations, and Future Implications in Genetic Research

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and other gene-editing technologies have revolutionized genetic research by enabling precise, targeted modifications of DNA sequences. This paper provides a comprehensive exploration of CRISPR technology, detailing its development, mechanism of action, and versatility in diverse applications. From advancements in medicine, including therapeutic interventions for genetic disorders, to innovations in agriculture aimed at enhancing crop resilience and yield, CRISPR's transformative potential is vast. However, the rapid evolution of gene editing presents significant ethical and societal challenges, particularly concerning human germline editing, ecological impacts, and issues of accessibility and equity. This paper examines these ethical considerations, emphasizing the need for robust regulatory frameworks and responsible scientific practices. It also projects the future trajectory of gene editing technologies, speculating on emerging trends, possible breakthroughs, and the global implications of CRISPR in fields such as personalized medicine, synthetic biology, and biotechnology. By critically analyzing current applications and addressing ethical concerns, this study aims to provide a balanced perspective on CRISPR's potential to reshape genetic research while advocating for ethical governance and public engagement in its ongoing development. CRISPR’s ability to target specific genes with high accuracy has made it an invaluable tool not only in research laboratories but also in clinical settings, where it shows promise in treating previously incurable diseases. Recent advancements have extended CRISPR’s applications beyond simple gene knockout, allowing for base editing, prime editing, and epigenetic modifications that expand the possibilities for genetic correction and enhancement. As scientists explore using CRISPR in complex organisms, the precision and control required for safe and effective treatments become a key focus, particularly in addressing off-target effects that could lead to unintended genetic consequences.

In situ visualization of endothelial cell-derived extracellular vesicle formation in steady state and malignant conditions.

Endothelial cells are integral components of all vasculature within complex organisms. As they line the blood vessel wall, endothelial cells are constantly exposed to a variety of molecular factors and shear force that can induce cellular damage and stress. However, how endothelial cells are removed or eliminate unwanted cellular contents, remains unclear. The generation of large extracellular vesicles (EVs) has emerged as a key mechanism for the removal of cellular waste from cells that are dying or stressed. Here, we used intravital microscopy of the bone marrow to directly measure the kinetics of EV formation from endothelial cells in vivo under homoeostatic and malignant conditions. These large EVs are mitochondria-rich, expose the 'eat me' signal phosphatidylserine, and can interact with immune cell populations as a potential clearance mechanism. Elevated levels of circulating EVs correlates with degradation ofthe bone marrow vasculature caused by acute myeloid leukaemia. Together, our study provides in vivo spatio-temporal characterization of EV formation in the murine vasculature and suggests that circulating, large endothelial cell-derived EVs can provide a snapshot of vascular damage at distal sites.

Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.

A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.

The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life.

A recent thought-provoking theory argues that complex organisms using epigenetic information for their normal development and functioning must irreversibly age as a result of epigenetic signal loss. Importantly, the scope of this theory could be considerably expanded, with scientific benefits, by analyzing epigenetic ageing beyond the borders of the Tree of Life. Viruses that use epigenetic signals for their normal functioning may also age, that is, present an increasing risk of failing to complete their individual life cycle and to disappear with time. As viruses are ancient, abundant, and infect a considerable diversity of hosts, the ageing virus hypothesis, if verified, would have important consequences for many fields of the Life sciences. Uncovering ageing viruses would integrate the most abundant and biologically central entities on Earth into theories of ageing, enhance virology, gerontology, evolutionary biology, molecular ecology, genomics, and possibly medicine through the development of new therapies manipulating viral ageing.

Acute toxicity of trypsin inhibitor from tamarind seeds in embryo and adult zebrafish (Danio rerio)

The trypsin inhibitor isolated from tamarind seeds (TTI) is being investigated for potential applications in the treatment of noncommunicable diseases (NCD), such as hypertension, obesity, and diabetes. This study aimed to assess TTI embryotoxicity and acute toxicity in adult zebrafish (Danio rerio). TTI was extracted and isolated from tamarind seeds. Embryonic and adult zebrafish were exposed for 96 hours to three concentrations of TTI (12.5, 25, and 50 mg/L). Zebrafish embryos (n=60 per group) were evaluated for survival, hatching, malformations, and potential developmental marker alterations, in addition to cardiotoxicity and neurotoxicity tests. For acute toxicity assessment in adults (n=20 per group), survival and locomotor and anxiety-like behaviors were assessed, along with genotoxicity (micronucleus) evaluation. Embryos exposed to TTI showed no significant adverse effects, presented normal heart rates and positive reflex response in the neurotoxicity tests. In adult fish, TTI did not cause mortality or significant behavioral changes, suggesting no neurotoxicity and no genotoxicity. Histopathological analyses of the whole body showed only changes in the liver and spinal cord, similar to those observed in the control group not exposed to TTI. These findings indicate TTI's biosafety and therapeutic potential in complex organisms. Further research is required to evaluate its long-term effects and efficacy in treating non-communicable diseases.

Agelessness is possible under the disposable soma theory but system complexity makes it unlikely

Although demographic studies have failed to find evidence of aging in certain animal species, classic evolutionary theories of aging struggle to explain how evolution could favor agelessness in such cases. Here, we develop mathematical models of the disposable soma theory to identify conditions in which agelessness would be evolutionarily favored. For any given type of damage that could accumulate and cause age-accelerating mortality risk, we find that evolution could select for its complete removal if the mortality risk it poses is severe enough and its repair does not pose too large of a penalty to reproduction. Environmental factors such as extrinsic mortality and the form of population density-dependent regulation also play a large role in determining the optimal rate of aging and whether agelessness should be evolutionarily favored. However, in a system with multiple sources of damage and multiple independent repair processes, avoiding aging is rarely evolutionarily favorable. Pleiotropic repair processes, such as those that could be present in asexual fissioning organisms, make agelessness more likely but do not guarantee it. Our results indicate that agelessness could be favored by evolution in narrow contexts but that multiple types of damage and repair make agelessness unlikely to arise in sufficiently complex organisms.

How oxygenation shapes immune responses: emerging roles for physioxia and pathological hypoxia.

Most eukaryotes require oxygen for their survival and, with increasing multicellular complexity, oxygen availability and delivery rates vary across the tissues of complex organisms. In humans, healthy tissues have markedly different oxygen gradients, ranging from the hypoxic environment of the bone marrow (where our haematopoietic stem cells reside) to the lungs and their alveoli, which are among the most oxygenated areas of the body. Immune cells are therefore required to adapt to varying oxygen availability as they move from the bone marrow to peripheral organs to mediate their effector functions. These changing oxygen gradients are exaggerated during inflammation, where oxygenation is often depleted owing to alterations in tissue perfusion and increased cellular activity. As such, it is important to consider the effects of oxygenation on shaping the immune response during tissue homeostasis and disease conditions. In this Review, we address the relevance of both physiological oxygenation (physioxia) and disease-associated hypoxia (where cellular oxygen demand outstrips supply) for immune cell functions, discussing the relevance of hypoxia for immune responses in the settings of tissue homeostasis, inflammation, infection, cancer and disease immunotherapy.

A short historical essay on the development of biology

The aim is to study the developmental stages of the science all living things – biology in the aspect on the concept of changes ideas about carriers of life: from the simplest to the most complex organism. Search-bibliographic and historical method, which allowed for determining the main steps in the chronological development of biology. Biology as a science was formed over the centuries in the ancient history of mankind thanks to efforts and achievements of the most outstanding scientists of different countries of the world. Scholars divide the history of the development of biology into several periods: heuristic or empirical, morphological or descriptive, microscopic, physiological and genetic. Such periodization is quite conditional. Separate periods sometimes coincide in time. Scientific discoveries that underlie this periodization at the same time, resulting in the parallel accumulation or relevant knowledge. The article present scientists who studied the biology of microorganisms, plants, fungi, animals, humans at all levels of their structural organization. The article reflects the history of the development of biology as a science in dates and names.

Биотестирование меламина с использованием многокомпонентной тест-системы

In recent decades, halogen-containing flame retardants have been gradually replaced by safer flame retardants, including nitrogen-containing compounds. However, their ecotoxicity is poorly studied. The ecotoxicity of melamine, a widely used nitrogen flame retardant, at concentrations equal to MPC in water (4 mg/L), 5 MPC (20 mg/L) and 10 MPC (40 mg/L) was assessed in this study using a complex of test organisms. The assessment of ecotoxicity using the dehydrogenase activity of Dietzia maris AM3 as a test microorganism revealed a stimulating effect of melamine at a concentration equivalent to the MPC; concentrations of 5 and 10 MPC inhibited the activity of dehydrogenases by 19.3% and 10.5%, respectively, indicating low toxicity. No toxic effects were observed on protococcal algae Chlorella vulgaris Beijer at any of the tested concentrations. The effect of melamine solutions on the mortality of crustaceans Daphnia magna Straus was noted only at a concentration of 10 MPC, and the mortality rate was 25%. Lemna growth inhibition test showed that melamine at concentrations equal to the MPC and 5 MPC had an inhibitory effect on the growth of Lemna minor L. It also caused a significant decrease (by 47–52%) in the total chlorophyll content in fronds when exposed to all studied concentrations of melamine.

IRescue: uncertainty-aware quantification of transposable elements expression at single cell level.

Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present IRescue (Interspersed Repeats single-cell quantifier), a software capable of estimating the expression of TE subfamilies at the single-cell level. IRescue incorporates a unique UMI deduplication algorithm to rectify sequencing errors and employs an Expectation-Maximization procedure to effectively redistribute the counts of multi-mapping reads. Our study showcases the precision of IRescue through analysis of both simulated and real single cell and nuclei RNA-seq data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection and recovery. By linking the expression patterns of TE signatures to specific conditions and biological contexts, we unveil insights into their potential roles in cellular heterogeneity and disease progression.

Swedana Karma (Sweating Therapy) - A Brief Review

The human body is among the most fascinating natural wonders. It is a highly complex multicellular organism whose life and well-being rely on appropriate homeostasis, coordination, and harmony between the self and environment. Ayurveda is the science of health; it offers therapeutic and preventive methods for restoring tissue homeostasis and helping people reach optimal health. Swedana, also known as body sweating, is a typical therapeutic technique used in Ayurvedic medicine. Swedana is recommended for its calming or cleansing properties throughout the traditional Ayurvedic scriptures. It can be performed as an independent intervention or as a prelude to Panchakarma, or the five detoxification procedures.

A Droplet-Based Microfluidic Platform for High-Throughput Culturing of Yeast Cells in Various Conditions.

Yeast plays a significant role in a variety of fields. In particular, it is extensively used as a model organism in genetics and cellular biology studies, and is employed in the production of vaccines, pharmaceuticals, and biofuels. Traditional "bulk"-based studies on yeast growth often overlook cellular variability, emphasizing the need for single-cell analysis. Micro-droplets, tiny liquid droplets with high surface-area-to-volume ratios, offer a promising platform for investigating single or a small number of cells, allowing precise control and monitoring of individual cell behaviors. Microfluidic devices, which facilitate the generation of micro-droplets, are advantageous due to their reduced volume requirements and ability to mimic in vivo micro-environments. This study introduces a custom-designed microfluidic device to encapsulate yeasts in micro-droplets under various conditions in a parallel manner. The results reveal that optimal glucose concentrations promoted yeast growth while cycloheximide and Cu2+ ions inhibited it. This platform enhances yeast cultivation strategies and holds potential for high-throughput single-cell investigations in more complex organisms.

IGF2BP1-Mediated Regulation of CCN1 Expression by Specific Binding to G-Quadruplex Structure in Its 3'UTR.

The intricate regulation of gene expression is fundamental to the biological complexity of higher organisms, and is primarily governed by transcriptional and post-transcriptional mechanisms. The 3'-untranslated region (3'UTR) of mRNA is rich in cis-regulatory elements like G-quadruplexes (G4s), and plays a crucial role in post-transcriptional regulation. G4s have emerged as significant gene regulators, impacting mRNA stability, translation, and localization. In this study, we investigate the role of a robust parallel G4 structure situated within the 3'UTR of CCN1 mRNA in post-transcriptional regulation. This G4 structure is proximal to the stop codon of human CCN1, and evolutionarily conserved. We elucidated its interaction with the insulin-like growth factor 2 binding protein 1 (IGF2BP1), a noncanonical RNA N6-methyladenosine (m6A) modification reader, revealing a novel interplay between RNA modifications and G-quadruplex structures. Knockdown experiments and mutagenesis studies demonstrate that IGF2BP1 binds specifically to the G4 structure, modulating CCN1 mRNA stability. Additionally, we unveil the role of IGF2BP1's RNA recognition motifs in G4 recognition, highlighting this enthalpically driven interaction. Our findings offer fresh perspectives on the complex mechanisms of post-transcriptional gene regulation mediated by G4 RNA secondary structures.

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

BackgroundSpatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in a single tissue slice and aligning or integrating multiple tissue slices originating from diverse sources for essential downstream analyses remains challenging. Numerous clustering, alignment, and integration methods have been specifically designed for ST data by leveraging its spatial information. The absence of comprehensive benchmark studies complicates the selection of methods and future method development.ResultsIn this study, we systematically benchmark a variety of state-of-the-art algorithms with a wide range of real and simulated datasets of varying sizes, technologies, species, and complexity. We analyze the strengths and weaknesses of each method using diverse quantitative and qualitative metrics and analyses, including eight metrics for spatial clustering accuracy and contiguity, uniform manifold approximation and projection visualization, layer-wise and spot-to-spot alignment accuracy, and 3D reconstruction, which are designed to assess method performance as well as data quality. The code used for evaluation is available on our GitHub. Additionally, we provide online notebook tutorials and documentation to facilitate the reproduction of all benchmarking results and to support the study of new methods and new datasets.ConclusionsOur analyses lead to comprehensive recommendations that cover multiple aspects, helping users to select optimal tools for their specific needs and guide future method development.

Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life.

Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.

Embryo Development in a Stochastic Universe.

Despite the elucidation of the many processes by which a single eukaryotic cell develops into a complex mature organism, it is still puzzling to some biologists how it is that an unvarying, interconnected set of processes becomes coordinated and insulated from a stochastic universe. This article suggests that electromagnetic processes deriving from the chemistry of an organism may provide such coordination. Specifically, the author develops the pacemaker concept, the periodic, autonomous electrical signal to the entire embryo, the result of which, after each pulse, is to alter or enlarge the transcriptome to produce the next level of complexity and maturity of the organism.

Topological Evolution of Simple and Complex Organisms: A Graph-Based Simulation Study on Adaptability and Evolutionary Constraints

Topological Evolution of Simple and Complex Organisms: A Graph-Based Simulation Study on Adaptability and Evolutionary Constraints