Organisms Research Articles

Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement.

Food safety is a global concern, with millions suffering from foodborne diseases annually. The World Health Organization (WHO) reports significant morbidity and mortality associated with contaminated food consumption, and this emphasizes the critical need for comprehensive food safety measures. Recent attention has turned to postbiotics, metabolic byproducts of probiotics, as potential agents for enhancing food safety. Postbiotics, including organic acids, enzymes, and bacteriocins, exhibit antimicrobial and antioxidant properties that do not require live organisms, and this offers advantages over probiotics. This literature review critically examines the role of postbiotics in gut microbiome modulation and applications in the food industry. Through an extensive review of existing literature, this study evaluates the impact of postbiotics on gut microbiome composition and their potential as functional food ingredients. Research indicates that postbiotics are effective in inhibiting food pathogens such as Staphylococcus aureus, Salmonella enterica, and Escherichia coli, as well as their ability to prevent oxidative stress-related diseases, and they also show promise as alternatives to conventional food preservatives that can extend food shelf life by inhibiting harmful bacterial growth. Their application in functional foods contributes to improved gut health and reduced risk of foodborne illnesses. Findings suggest that postbiotics hold promise for improving health and preservation by inhibiting pathogenic bacteria growth and modulating immune responses.

Intraspecific Shape Analysis of Bali Sardinella (Sardinella lemuru) Using Geometric Morphometrics Collected in the Coast of Cabadbaran, Agusan Del Norte, Philippines

Modern techniques are often applied to analyze the body shape differences among biological organisms. Also, taxonomy and systematics are two essential fields of Biology concerning shape discrimination. This study aims to identify the shape variations of Sardinella lemuru (Bali sardinella) using Symmetry Asymmetry Geometric Data (SAGE) Software Application. A total of 70 fish samples consisting of 35 males and 35 females were collected in Barangay Caasinan, Cabadbaran, Agusan Del Norte, Philippines. Standard laboratory procedures were done and fish samples were subjected to the analysis. Procrustes ANOVA revealed a highly significant difference (P<0.0001) among the components analyzed (individuals, sides, and individuals vs. sides). This implied that each of the fish samples exhibited different body shapes. Principal Component Analysis (PCA) obtained a high rate of Interaction/Fluctuating Asymmetry (76.79%) in males when compared to female samples (74.08%). The shape dissimilarities within the populations were associated with genetic components, ecological adaptations-swimming, predator escape, and resource competition. Thus, the present study identified shape disparity within the fish populations. The development of employing modern techniques enhances scientific methods to quantify shape dissimilarities among species individuals and assemblages.

E-Polymers: Applications in Biological Interfaces and Organisms

Future electronics will play a more critical role in people’s lives, as reflected in the realization of advanced human–machine interfaces, disease detection, medical treatment, and health monitoring. The current electronic products are rigid, non-degradable, and cannot repair themselves. Meanwhile, the human body is soft, dynamic, stretchable, degradable, and self-healing. Consequently, it is valuable to develop new electronic materials with skin-like properties that include stretchability, inhibition of invasive reactions, self-healing, long-term durability, and biodegradability. These demands have driven the development of a new generation of electronic materials with high-electrical performance and skin-like properties, among which e-polymers are increasingly being more extensively investigated. This review focuses on recent advances in synthesizing e-polymers and their applications in biointerfaces and organisms. Discussions include the synthesis and properties of e-polymers, the interrelationships between engineered material structures and human interfaces, and the application of implantable and wearable systems for sensors and energy harvesters. The final section summarizes the challenges and future opportunities in the evolving materials and biomedical research field.

Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology.

Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.

Should probiotics be administered as an adjunctive treatment along with antidepressants for major depressive disorder?

Madam, Major depressive disorder (MDD) is a significant factor in global disability rates and contributes significantly to the overall disease burden worldwide. According to estimates, approximately 3.8% of the global population is impacted, with a prevalence of 5.0% among adults and 5.7% among adults aged 60 years and above [1]. It is also the leading cause of suicide among individuals. While the administration of antidepressants is the widely known and successful treatment for this mental disorder, recent research and accumulating evidence have demonstrated that probiotics also function effectively in controlling anxiety and depression. Probiotics that provide psychological benefits are now referred to as psychobiotics. Psychobiotics are defined as live organisms that, when consumed in sufficient quantities, produce unexpected health benefits in individuals with psychiatric disorders [2]. Around 30% of patients with major depressive disorder (MDD) do not respond to traditional antidepressant medications targeting monoamine pathways, indicating the involvement of other biological mechanisms in the development of MDD [3]. One particularly promising hypothesis regarding the pathogenesis of MDD is the dysfunction of the gut-brain axis (GBA), with the gut microbiota playing a crucial role [4]. Numerous studies have investigated the impact of probiotics on stress resilience. The recent meta-analysis discovered a significant finding: when probiotics were combined with antidepressants, they showed a remarkable reduction in depressive symptoms. However, when used alone, probiotics exhibited a less impact on alleviating depressive symptoms. This highlights the crucial role of combining probiotics with standard treatments for a more substantial effect on managing depression [5]. These impressive results elucidate the advantages of administering probiotic strains in individuals suffering from mental health disorders, specifically MDD, by effectively addressing the imbalance within the gut-brain axis (GBA) and suppressing stress-induced activation of biological pathways involved in psychological disturbances. Recurrent evidence has proven that gut microbiota play a significant role in neuronal homeostasis and any imbalance may contribute as a factor in the underlying mechanism of the pathogenesis of MDD. Henceforth, further research should be encouraged in order to develop promising microbiome-based therapeutics for MDD, and physicians should consider administering probiotics as an adjunctive treatment for depression alongside antidepressants. Moreover, the importance of probiotics should be thoroughly studied, and medical doctors should raise awareness of the significance of the gut-brain axis and associated biological pathways, which play a major role in an individual's mental health.

Potentiality of natural live food organisms in shrimp culture: A review

The aquaculture industry is growing quickly due to increased fish consumption and a decline in wild fish catch. About half of the world's seafood demand for human consumption is now met by farmed seafood. The aquafeed market is expanding along with the aquaculture sector. Some of the elements in shrimp feed are derived from terrestrial plants and low-value forage fishes (fish meal). It is impossible to produce more fish meals since doing so would harm the ocean's environment and sustainability. The reduction in shrimp feed cost can also be done by introducing low-cost, environment-friendly ingredients in shrimp feed formulation. Therefore, new and ecologically friendly shrimp (Litopenaeus vannamei) feed component sources must be created. Live food organisms are a preferable option for this since they provide a variety of essential amino acids and beneficial triglycerides like fat, vitamins, and colors in their cell metabolites. Microalgae biomasses also represent feasible ingredients for shrimp feed sources. Their distinctive variety of bioactive chemicals can enhance color and pellet quality, act as a bulk element in shrimp feed, and boost the viability of farmed species. Live food organisms have a great economic potential since they have the highest biomass productivity of all photosynthetic organisms. In addition to giving farmers and exporters a better choice for feeding their fish, the availability of on-grown live food would also open up the prospect of improving the performance and quality of the fish and shrimp through bioencapsulation. This review study examines the possibility of generating natural food biomass as a component in shrimp feed.

Why Is Biological Teleology Non-constitutive (Merely Regulative) for Kant?

There is no doubt that Kant assigns a merely regulative function to biological teleology. But the reasons for Kant’s doing so are less clear. For some Kant scholars, Kant does so because, for him, the concept of natural purpose amounts at best to a subjective maxim of certain heuristic values. Appealing as it is, this view runs into difficulties when other Kant scholars note that Kant takes biological teleology to be indispensable and uses the natural purpose concept to identify biological organisms (or, more precisely speaking, formative powers). I argue that Kant treats biological teleology as non-constitutive (i.e., merely regulative), because the concept of natural purpose is not associated with any supporting laws (biological organisms as instances or particulars of the concept of natural purpose are given, but the concept itself as a universal is only assumed).

From reinforcement learning to agency: Frameworks for understanding basal cognition

Organisms play, explore, and mimic those around them. Is there a purpose to this behavior? Are organisms just behaving, or are they trying to achieve goals? We believe this is a false dichotomy. To that end, to understand organisms, we attempt to unify two approaches for understanding complex agents, whether evolved or engineered. We argue that formalisms describing multiscale competencies and goal-directedness in biology (e.g., TAME), and reinforcement learning (RL), can be combined in a symbiotic framework. While RL has been largely focused on higher-level organisms and robots of high complexity, TAME is naturally capable of describing lower-level organisms and minimal agents as well. We propose several novel questions that come from using RL/TAME to understand biology as well as ones that come from using biology to formulate new theory in AI. We hope that the research programs proposed in this piece shape future efforts to understand biological organisms and also future efforts to build artificial agents.

Correlative atomic force microscopy and scanning electron microscopy of bacteria-diamond-metal nanocomposites

Research investigating the interface between biological organisms and nanomaterials nowadays requires multi-faceted microscopic methods to elucidate the interaction mechanisms and effects. Here we describe a novel approach and methodology correlating data from an atomic force microscope inside a scanning electron microscope (AFM-in-SEM). This approach is demonstrated on bacteria-diamond-metal nanocomposite samples relevant in current life science research. We describe a procedure for preparing such multi-component test samples containing E. coli bacteria and chitosan-coated hydrogenated nanodiamonds decorated with silver nanoparticles on a carbon-coated gold grid. Microscopic topography information (AFM) is combined with chemical, material, and morphological information (SEM using SE and BSE at varied acceleration voltages) from the same region of interest and processed to create 3D correlative probe-electron microscopy (CPEM) images. We also establish a novel 3D RGB color image algorithm for merging multiple SE/BSE data from SEM with the AFM surface topography data which provides additional information about microscopic interaction of the diamond-metal nanocomposite with bacteria, not achievable by individual analyses. The methodology of CPEM data interpretation is independently corroborated by further in-situ (EDS) and ex-situ (micro-Raman) chemical characterization as well as by force volume AFM analysis. We also discuss the broader applicability and benefits of the methodology for life science research.

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR interference sequencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii. Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

Automating methods for estimating metabolite volatility.

The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called volcalc that uses chemoinformatic tools to automate these volatility estimates for all metabolites in an extensive and continuously updated pathway database: the Kyoto Encyclopedia of Genes and Genomes (KEGG) that connects metabolites, organisms, and reactions. We first benchmark the automated pipeline against a manually curated data set and show that the same category of volatility (e.g., nonvolatile, low, moderate, high) is predicted for 93% of compounds. We then demonstrate how volcalc might be used to generate and test hypotheses about the role of volatility in biological systems and organisms. Specifically, we estimate that 3.4 and 26.6% of compounds in KEGG have high volatility depending on the environment (soil vs. clean atmosphere, respectively) and that a core set of volatiles is shared among all domains of life (30%) with the largest proportion of kingdom-specific volatiles identified in bacteria. With volcalc, we lay a foundation for uncovering the role of the volatilome using an approach that is easily integrated with other bioinformatic pipelines and can be continually refined to consider additional dimensions to volatility. The volcalc package is an accessible tool to help design and test hypotheses on volatile metabolites and their unique roles in biological systems.

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes.

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR interference sequencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii. Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

Agrobiodiversity-Based Landscape Design in Urban Areas.

Agrobiodiversity represents a system of biological organisms that contribute to agri-food production. In a context marked by a significant loss of food-relevant species and a reduction in their genetic diversity, the adoption of strategies to preserve and enhance the diversity of genetic resources that support and complement agricultural production has become a global challenge. Many sustainable development strategies outlined in recent years directly and indirectly attribute a crucial role to agrobiodiversity in meeting food needs, ensuring food system security, promoting food justice, and enhancing well-being in modern living environments. This contribution aims to analyze the process of knowledge and awareness that has led many cities to plan their urban development by investing in the agricultural matrix and to address the design of open spaces with agricultural biodiversity.

Potential economic impact on U.S. aquaculture of injurious species listing of major aquaculture species

AbstractRegulatory changes to the Lacey Act and recent petitions to add aquaculture species in trade to the list of injurious wildlife could lead to prohibitions of interstate movement of live aquatic organisms with the potential for unintended, negative economic consequences. In this analysis, the economic impact of the potential federal prohibition of interstate transport of seven aquaculture species (blue catfish, tilapia, red swamp crawfish, grass carp, koi, guppy, and goldfish) currently in trade was assessed. Total economic impact was estimated to be $452 million (USD) annually, with a loss of 4819 jobs and a loss of $35 million in tax revenue. Effects could potentially occur on the largest sectors of U.S. aquaculture in as many as 80% of U.S. states and result in negative economic effects on as much as 21% of U.S. aquaculture farms.

Deep learning reduces data requirements and allows real-time measurements in imaging FCS

Imaging fluorescence correlation spectroscopy (FCS) is a powerful tool to extract information on molecular mobilities, actions, and interactions in live cells, tissues, and organisms. Nevertheless, several limitations restrict its applicability. First, FCS is data hungry, requiring 50,000 frames at 1-ms time resolution to obtain accurate parameter estimates. Second, the data size makes evaluation slow. Third, as FCS evaluation is model dependent, data evaluation is significantly slowed unless analytic models are available. Here, we introduce two convolutional neural networks—FCSNet and ImFCSNet—for correlation and intensity trace analysis, respectively. FCSNet robustly predicts parameters in 2D and 3D live samples. ImFCSNet reduces the amount of data required for accurate parameter retrieval by at least one order of magnitude and makes correct estimates even in moderately defocused samples. Both convolutional neural networks are trained on simulated data, are model agnostic, and allow autonomous, real-time evaluation of imaging FCS measurements.

METHODS OF GENETIC TRANSFORMATION: MAJOR EMPHASIS TO CROP PLANTS

Advancements in gene transfer technology have indeed opened up exciting possibilities for more effectively manipulating the genetic makeup of live organisms, ranging from microorganisms to plants and animals. Direct and indirect transformations are the two basic types of gene transfer techniques. Indirect method comprises Agrobacterium mediated method as it involves intermediate host between gene of interest and target and this method is most opted one out of all present. Direct gene transformation methods, on the other hand, do not involve the use of an intermediate host organism. Instead, they rely on physical means to transfer genes between cells. Biolistic transformation uses high-velocity particles to deliver DNA into target cells, while microinjection and macroinjection involve the direct injection of DNA into cells. Protoplast fusion combines the genetic material of two different cells by fusing their protoplasts. Natural methods for gene transfer encompass mechanisms that occur naturally in various organism, includes transposition, conjugation, phage and retroviral transductions and bacterial transformation. Chemical techniques utilize chemical agents to facilitate gene transfer, such as calcium phosphate-mediated transformation, polyethylene glycol (PEG)-mediated transformation, DEAE (Diethylethanolamine)-Dextran-mediated transformation. Genes can be also being transferred using electrical techniques such as electroporation and electrofusion. Crop improvement and trait improvement are now being hastened by the fast-rising number of sequenced plant genomes, information from functional genomics data to understand gene function, innovative gene cloning, and tissue culture techniques. Despite being indispensable, its progress is still hindered by the fact that many plant species and agricultural genotypes exhibit low transformability or are resistant to established tissue culture and regeneration conditions. Here, we review the techniques employed in plant transformation and provide a concise overview of their evolution in agricultural crops, from their first inception to present time.

Characterization of trade-offs between immunity and reproduction in the coral species Astrangia poculata.

Living organisms face ubiquitous pathogenic threats and have consequently evolved immune systems to protect against potential invaders. However, many components of the immune system are physiologically costly to maintain and engage, often drawing resources away from other organismal processes such as growth and reproduction. Evidence from a diversity of systems has demonstrated that organisms use complex resource allocation mechanisms to manage competing needs and optimize fitness. However, understanding of resource allocation patterns is limited across taxa. Cnidarians, which include ecologically important organisms like hard corals, have been historically understudied in the context of resource allocations. Improving understanding of resource allocation-associated trade-offs in cnidarians is critical for understanding future ecological dynamics in the face of rapid environmental change. Here, we characterize trade-offs between constitutive immunity and reproduction in the facultatively symbiotic coral Astrangia poculata. Male colonies underwent ex situ spawning and sperm density was quantified. We then examined the effects of variable symbiont density and energetic budget on physiological traits, including immune activity and reproductive investment. Furthermore, we tested for potential trade-offs between immune activity and reproductive investment. We found limited associations between energetic budget and immune metrics; melanin production was significantly positively associated with carbohydrate concentration. However, we failed to document any associations between immunity and reproductive output which would be indicative of trade-offs, possibly due to experimental limitations. Our results provide a preliminary framework for future studies investigating immune trade-offs in cnidarians.

A near-infrared fluorescent probe for rapid and on-site detection of sulfur dioxide derivative in biological, food and environmental systems

Emission of toxic gaseous sulfur dioxide (SO2) and its derivative bisulfite (HSO3–) from various industrial applications, like food processing, transportation, and the coking process, has raised substantial concerns regarding environmental quality and public health. The probes for specific and sensitive detection of SO2 derivatives plays an essential role in their regulation, and ultimately mitigating their environmental and health implications, but the one that can detect SO2 derivatives onsite by end users remains limited. Herein, we report a new near-infrared fluorescence probe (SL) for rapid and onsite detection of SO2 derivative, HSO3– in industrial wastewater, food samples and for sensing its interaction with biological organisms. The SL is developed through coupling of quinolinium and coumarin moiety through an electron deficit CC bond that can specifically react with HSO3− via a Michael addition. By recording the blue shift of absorption and emission spectra, SL can sensitively detect HSO3– (limit of detection, 38 nM) in aqueous solution within 40 s SL is biocompatible, can be used for evaluating toxicity of SO2 derivatives in living organisms. The preparation of SL-stained test paper allows the colorimetric/fluorometric analysis for quantification of HSO3– onsite in food, river and coking wastewater samples using a smartphone. The successful development of SL not only provides a new tool to investigate HSO3– in biological, food and environmental systems, but also potentially promotes the application of fluorescence technique for rapid and onsite analysis of real-world samples by end users.

Digital Mechanical Metamaterial: Encoding Mechanical Information with Graphical Stiffness Pattern for Adaptive Soft Machines.

Inspired by the adaptive features exhibited by biological organisms like the octopus, soft machines that can tune their shape and mechanical properties have shown great potential in applications involving unstructured and continuously changing environments. However, current soft machines are far from achieving the same level of adaptability as their biological counterparts, hampered by limited real-time tunability and severely deficient reprogrammable space of properties and functionalities. As a steppingstone toward fully adaptive soft robots and smart interactive machines, an encodable multifunctional material that uses graphical stiffness patterns is introduced here to in situ program versatile mechanical capabilities without requiring additional infrastructure. Through independently switching the digital binary stiffness states (soft or rigid) of individual constituent units of a simple auxetic structure with elliptical voids, in situ and gradational tunability is demonstrated here in various mechanical qualities such as shape-shifting and -memory, stress-strain response, and Poisson's ratio under compressive load as well as application-oriented functionalities such as tunable and reusable energy absorption and pressure delivery. This digitally programmable material is expected to pave the way toward multienvironment soft robots and interactive machines.

Genome-wide identification and expression analysis of cytochrome P450 gene family in Macrobrachium nipponense

Cytochrome P450 (CYP450) is a superfamily widely found in various biological organisms, including animals, plants, and microorganisms. CYP450 is involved in the metabolism of endogenous and exogenous substances. In addition, a few CYP450 genes named as Halloween genes (CYP302a1, CYP307a1, etc.) are associated with the synthesis and secretion of ecdysone in Arthropods. Macrobrachium nipponense (Arthropoda, Crustacean) has many excellent breeding characteristics; for example, rapid growth rate, ability to survive in a variety of environments and high economic value. In order to further explored the structure and function of CYP450, a genome-wide analysis of CYP450 gene family was performed in M. nipponense. A total of 67 CYP450 genes were identified, and extensive bioinformatic analysis methods were conducted, including physicochemical property, sequence alignment, evolutionary tree construction, conserved sequence, chromosome localization, protein-protein interactions, and quantitative expression. The results showed that most CYP450 genes being around 500 amino acids, with 25 tandem repeats genes. The majority of CYP450 genes have the signature structure of the CYP450 gene family to ensure the stability of the spatial structure and the ability to bind substrates. The Halloween genes and CYP18a1 sequences are similar and occupy an importance role in M. nipponense. Finally, most CYP450 genes were up-regulated in gill and hepatopancreas of M. nipponense under acute high temperature stress, with significant up-regulation of Halloween gene expression. This study could further deepen the understanding of the structure and function of CYP450 in M. nipponense and investigate the role of CYP450 in freshwater crustaceans under high temperatures.