Biological Interest Research Articles

Cenozoic history of the tropical marine biodiversity hotspot

The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation–extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.

THE INFLUENCE OF EXTRACURRICULAR ACTIVITIES ON THE INTEREST OF CZECH AND FINNISH STUDENTS IN BIOLOGY

Extracurricular learning plays a key role in shaping students' interest in (not only) biology. The research examined which extracurricular areas related to biology can make biology more attractive for the participating Finnish and Czech students. A 5-point Likert scale questionnaire was administered to 178 Finnish and 195 Czech 9th-grade lower-secondary school students. Cronbach's alpha, Varimax rotation and Mann–Whitney U-test were performed. Factor analysis identified 7 areas: Family trips, My career, Biology lessons, Healthy lifestyle, Institutions, Nature-related hobbies, and Information sources. For Czech, hobbies related to nature and family trips are significant contributors to fostering interest in biology, and an informal educational environment is crucial for cultivating a lasting relationship with biology. For Finns, biology classes and career orientation have a more significant influence on students, demonstrating the effectiveness of formal educational strategies in increasing students' interest in biology. Increasing interest in biology among the students observed in both sociocultural environments is significantly influenced by family involvement and the use of information sources. Further research should explore how specific ECA can support the connection between family and school environments and their impact on students' interest and engagement in biology lessons. Keywords: extracurricular activities, interest in biology, lower secondary school students, questionnaire

Modular Fluorescent Cholesterol Naphthalimide Probes And Their Application For Cholesterol Trafficking Studies In Cells.

Development of fluorescent cholesterol analogs to better understand subcellular cholesterol trafficking is of great interest for cell biology and medicine. Our approach utilizes a bifunctional 1,8-naphthalimide scaffold with a push-pull character, modified on one side with a head group and a linker on the other side connecting it to cholesterol via an ester bond. Through structure-function studies, we've explored how different substituents-linkers and head groups-affect the ability of these fluorescent cholesterol naphthalimide analogs (CNDs) to mimic natural cholesterol behavior at both molecular and cellular levels. We categorized the resulting analogs into three groups: neutral, charged, and those featuring a hydroxyl group. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Extensive all-atom molecular dynamics simulations helped us examine how these analogs perform in model membranes compared to cholesterol. Additionally, we investigated the partitioning of these fluorescent probes in phase-separated giant unilamellar vesicles. We evaluated the uptake and distribution of these probes within mouse fibroblast cells and astrocytes, for their subcellular distributions in lysosomes and compared that to BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of the fluorescent probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesterol probes bearing distinct spectral, biophysical, and cellular targeting features, which makes it a valuable toolkit for the investigation of subcellular distribution and trafficking of cholesterol and its derivatives.

Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability.

Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient (FBAL-ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL-ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL-ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL-ANC could be remarkably enhanced. The relationship between FBAL-ANC and other pedigree-based parameters is also discussed.

Use of CRISPRoff and synthetic Notch to modulate and relay endogenous gene expression programs in engineered cells.

Uncovering the stimulus-response histories that give rise to cell fates and behaviors is an area of great interest in developmental biology, tissue engineering, and regenerative medicine. A comprehensive accounting of cell experiences that lead to the development of organs and tissues can help us to understand developmental anomalies that may underly disease. Perhaps more provocatively, such a record can also reveal clues as to how to drive cell collective decision-making processes, which may yield predictable cell-based therapies or facilitate production of tissue substitutes for transplantation or in vitro screening of prospective therapies to mitigate disease. Toward this end, various methods have been applied to molecularly trace developmental trajectories and record interaction histories of cells. Typical methods involve artificial gene circuits based on recombinases that activate a suite of fluorescent reporters or CRISPR-Cas9 genome writing technologies whose nucleic acid-based record keeping serves to chronicle cell-cell interactions or past exposure to stimuli of interests. Exciting expansions of the synthetic biology toolkit with artificial receptors that permit establishment of defined input-to-output linkages of cell decision-making processes opens the door to not only record cell-cell interactions, but to also potentiate directed manipulation of the outcomes of such interactions via regulation of carefully selected transgenes. Here, we combine CRISPR-based strategies to genetically and epigenetically manipulate cells to express components of the synthetic Notch receptor platform, a widely used artificial cell signaling module. Our approach gives rise to the ability to conditionally record interactions between human cells, where the record of engagement depends on expression of a state-specific marker of a subset of cells in a population. Further, such signal-competent interactions can be used to direct differentiation of human embryonic stem cells toward pre-selected fates based on assigned synNotch outputs. We also implemented CRISPR-based manipulation of native gene expression profiles to bias outcomes of cell engagement histories in a targeted manner. Thus, we present a useful strategy that gives rise to both state-specific recording of cell-cell interactions as well as methods to intentionally influence products of such cell-cell exchanges.

Squaramide Formation for DNA-Encoded Library Synthesis.

DNA-encoded libraries (DELs) can be considered as one of the most powerful tools for the discovery of small molecules of biological interest. However, the ability to access large DELs is contingent upon having chemical transformations that work in aqueous phase and generate minimal DNA alterations and the availability of building blocks compatible with on-DNA chemistry. In addition, accessing scaffolds of interest to medicinal chemists can be challenging in a DEL setting because of inherent limitations of DNA-supported chemistry. In this context, a squaramide formation reaction was developed by using a two-step process. The mild and high-yielding reaction tolerates a wide array of functional groups and was shown to be safe for DNA, thereby making this methodology ideal for DELs.

Comprehensive Strategies for the Synthesis of 1,3-Enyne Derivatives

AbstractThe synthesis of 1,3-enyne has widespread appeal in organic synthesis due to their proven adaptability as intermediates in routes to compounds of significant biological and material interest. A variety of methods have been designed to formulate 1,3-enynes from diverse substrates, such as alkynes, 1,3-diynes, alkynyl-substituted cyclopropanes, and propargyl alcohols. This review covers the synthesis of 1,3-enynes utilizing the homo- and cross-coupling of alkynes, nucleophilic metal/acid-induced cyclopropane ring opening, and rearrangement/dehydration of propargyl alcohols. A key concern in procedures starting from alkynes and 1,3-diynes is the management of regio-, stereo-, and, where fitting, chemoselectivity. In contrast, in cyclopropyl ring opening nucleophile orientation determines the 1,3-enynes formed. Efficient methods for the broad and selective synthesis of 1,3-enynes are highlighted and specific examples are given to demonstrate the efficacy of these processes.1 Introduction and Scope2 Synthesis2.1 Synthesis of 1,3-Enynes from Alkynes2.1.1 Metal-Catalyzed Cross-Coupling/Additions of Alkynes with Alkenes or Vinyl or Aryl Halides2.1.1.1 Palladium Catalysis2.1.1.2 Rhodium Catalysis2.1.1.3 Copper Catalysis2.1.1.4 I ron Catalysis2.1.1.5 Nickel Catalysis2.1.1.6 Miscellaneous2.2 Synthesis of Enynes from Propargyl Alcohols2.3 Metal/Acid-Catalyzed Ring Opening of Cyclopropanes3 Conclusion

Recent Advances in the Therapeutic Potential of Carotenoids in Preventing and Managing Metabolic Disorders.

Carotenoids constitute compounds of significant biological interest due to their multiple biological activities, such as antimicrobial, anticancer, antiadipogenic, antidiabetic, and antioxidant properties. Metabolic syndrome (MetS) comprehends a series of metabolic abnormalities (e.g., hypertension, obesity, and atherogenic dyslipidemia) that can affect children, adolescents, and the elderly. The treatment of MetS involves numerous medications, which, despite their efficacy, pose challenges due to prolonged use, high costs, and various side effects. Carotenoids and their derivatives have been proposed as alternative treatments to MetS because they reduce serum triglyceride concentrations, promote insulin response, inhibit adipogenesis, and downregulate angiotensin-converting enzyme activity. However, carotenoids are notably sensitive to pH, light exposure, and temperature. This review addresses the activity of carotenoids such as lycopene, lutein, fucoxanthin, astaxanthin, crocin, and β-carotene towards MetS. It includes a discussion of sources, extraction methods, and characterization techniques for analyzing carotenoids. Encapsulation approaches are critically reviewed as alternatives to prevent degradation and improve the biological performance of carotenoids. A brief overview of the physiopathology and epidemiology of the diseases, including MetS, is also provided.

Microwave-assisted Solvent-free Synthesis of Some New 4-[2-(Substituted phenyl)-4, 5-diphenyl-1H-imidazole-1-yl]-1H-indoles of Biological Interest

Microwave-assisted Solvent-free Synthesis of Some New 4-[2-(Substituted phenyl)-4, 5-diphenyl-1H-imidazole-1-yl]-1H-indoles of Biological Interest

A personal reflection on Bowen family systems theory by Dr Michael Kerr

AbstractThis interview with Dr Michael Kerr highlights his ongoing interest in science, biology and neuroscience. Guided by Bowen family systems theory, Dr Kerr's observations examine how research is showing links between physical health, the immune response and psychological motivation and wellbeing. Wellbeing is compromised in less adaptive families, which succumb more easily to any anxiety generated outside the family, as well as the chronic anxiety generated within the family. Amid times of societal regression, the capacity to adapt in a way that promotes survival and wellbeing depends on the level of differentiation of self. Differentiation of self is the sum of the capacity to maintain emotional objectivity, emotional neutrality and to take action. Psychiatrist, Dr Michael (Mike) Kerr, who more recently published Bowen Theory's Secrets: Revealing the hidden lives of families (2019), co‐authored the seminal work on Bowen family systems theory, Family Evaluation, in 1988 with Dr Murray Bowen. From 1990 to 2011, after Dr Bowen's death, Mike was the Director of the Bowen Center for the Study of the Family in Washington, DC. He is passionate about the relationship between differentiation of self, illness and the family emotional process and how this relates to the biological and evolutionary processes that operate in non‐human species. Mike developed the unidisease concept and is well known for his work interviewing Dr Murray Bowen on Bowen family systems theory between 1979 and 1986 for the Bowen‐Kerr Interview Series. A special issue on Bowen theory would not be complete without a commentary from Mike. So, in this interview with Bowen family systems therapist, Dr Linda MacKay, Mike discusses his life effort to research and apply Bowen theory.

Βiomarkers of aging

The phenomenon of longevity and healthy aging as well as the factors that can slow down or even prevent the appearance of pathological conditions related to aging is a subject of interest in modern biology and medical research. In this context, a series of clinical and biochemical indicators are recorded and evaluated, as well as a wide variety of cellular aging biomarkers that include molecular signals and biomolecules at the proteomic, metabolomic, genomic and epigenetic level. The use of biomarkers to assess biological aging can help predict life expectancy and quality of life. The reliability of various biomarkers of aging should also be tested for validity against clinical markers of aging, such as frailty, loss of (physical) function, chronic diseases and disabilities.

Extraction methods of polysaccharides, peptides, pigments, polyphenols from red and brown algae and their use in the treatment of skin hyperpigmentation and wrinkling

The phenomenon of longevity and healthy aging as well as the factors that can slow down or even prevent the appearance of pathological conditions related to aging is a subject of interest in modern biology and medical research. In this context, a series of clinical and biochemical indicators are recorded and evaluated, as well as a wide variety of cellular aging biomarkers that include molecular signals and biomolecules at the proteomic, metabolomic, genomic and epigenetic level. The use of biomarkers to assess biological aging can help predict life expectancy and quality of life. The reliability of various biomarkers of aging should also be tested for validity against clinical markers of aging, such as frailty, loss of (physical) function, chronic diseases and disabilities.

Relating absorbing and hard wall boundary conditions for a one-dimensional run-and-tumble particle

The connection between absorbing boundary conditions and hard walls is well established in the mathematical literature for a variety of stochastic models, including for instance the Brownian motion. In this paper we explore this duality for a different type of process which is of particular interest in physics and biology, namely the run-tumble-particle, a toy model of active particle. For a one-dimensional run-and-tumble particle (RTP) subjected to an arbitrary external force, we provide a duality relation between the exit probability, i.e. the probability that the particle exits an interval from a given boundary before a certain time t, and the cumulative distribution of its position in the presence of hard walls at the same time t. We show this relation for a RTP in the stationary state by explicitly computing both quantities. At finite time, we provide a derivation using the Fokker–Planck equation. All the results are confirmed by numerical simulations.

Population Dependent Two-Sex Branching Process with Random Mating and Overlapping Generations

Abstract This research focuses on stochastic modeling of the evolution over time of biological populations through branching processes. We introduce a new class of discrete time two-sex branching processes with random mating and overlapping generations. Mating and reproduction are considered to be influenced by the numbers of females and males existing in the population. This evolution over time with generational overlap is a novel research in two-sex branching process literature. We study general probabilistic properties and establish some limiting results of biological interest.

CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo

AbstractCaenorhabditis elegans has been widely used as a model organism in developmental biology due to its invariant development. In this study, we developed a desktop software CShaperApp to segment fluorescence‐labeled images of cell membranes and analyze cellular morphologies interactively during C. elegans embryogenesis. Based on the previously proposed framework CShaper, CShaperApp empowers biologists to automatically and efficiently extract quantitative cellular morphological data with either an existing deep learning model or a fine‐tuned one adapted to their in‐house dataset. Experimental results show that it takes about 30 min to process a three‐dimensional time‐lapse (4D) dataset, which consists of 150 image stacks at a ∼1.5‐min interval and covers C. elegans embryogenesis from the 4‐cell to 350‐cell stages. The robustness of CShaperApp is also validated with the datasets from different laboratories. Furthermore, modularized implementation increases the flexibility in multi‐task applications and promotes its flexibility for future enhancements. As cell morphology over development has emerged as a focus of interest in developmental biology, CShaperApp is anticipated to pave the way for those studies by accelerating the high‐throughput generation of systems‐level quantitative data collection. The software can be freely downloaded from the website of Github (cao13jf/CShaperApp) and is executable on Windows, macOS, and Linux operating systems.

Nonlinear modeling of oral glucose tolerance test response to evaluate associations with aging outcomes.

As people age, their ability to maintain homeostasis in response to stressors diminishes. Physical frailty, a syndrome characterized by loss of resilience to stressors, is thought to emerge due to dysregulation of and breakdowns in communication among key physiological systems. Dynamical systems modeling of these physiological systems aims to model the underlying processes that govern response to stressors. We hypothesize that dynamical systems model summaries are predictive of age-related declines in health and function. In this study, we analyze data obtained during 75-gram oral-glucose tolerance tests (OGTT) on 1,120 adults older than 50 years of age from the Baltimore Longitudinal Study on Aging. We adopt a two-stage modeling approach. First, we fit OGTT curves with the Ackerman model-a nonlinear, parametric model of the glucose-insulin system-and with functional principal components analysis. We then fit linear and Cox proportional hazards models to evaluate whether usual gait speed and survival are associated with the stage-one model summaries. We also develop recommendations for identifying inadequately-fitting nonlinear model fits in a cohort setting with numerous heterogeneous response curves. These recommendations include: (1) defining a constrained parameter space that ensures biologically plausible model fits, (2) evaluating the relative discrepancy between predicted and observed responses of biological interest, and (3) identifying model fits that have notably poor model fit summary measures, such as [Formula: see text], relative to other fits in the cohort. The Ackerman model was unable to adequately fit 36% of the OGTT curves. The stage-two regression analyses found no associations between Ackerman model summaries and usual gait speed, nor with survival. The second functional principal component score was associated with faster gait speed (p<0.01) and improved survival (p<0.01).

Sight and blindness: The relationship between ostracod eyes, water depth, and light availability in the Arctic Ocean

AbstractEye loss has been a long‐standing interest in evolutionary biology. Many organisms that inhabit environments without light penetration, for example the deep sea, exhibit eye loss and thus become blind. However, water‐depth distribution of eyes in marine organisms is poorly understood. Ostracods are widely distributed crustaceans, and many sighted marine ostracods have eye tubercles (lenses) on their shells. Since eye tubercles are visible on the shells illustrated in much literature, it is easy to determine their presence or absence via a literature survey. Here, we used a large Arctic‐wide ostracod census dataset (Arctic Ostracode Database) to calculate the eye index (the percentage of species with eyes), and compare them with water depth and light availability. As water depth increases, eye index values decrease and become constantly zero in water deeper than 1000 m. Similar decline of sighted species with increasing depth is also known in isopods and amphipods, suggesting that it may be common in other crustaceans and perhaps in deep‐sea organisms in general. We also show that eye index values increase as light availability increases. This study is the first to quantify how distributions of sighted and blind species change with light availability, giving baseline information on vision in the deep sea.

Bringing cell biology into classroom: tips to culture and observe skeletal muscle cells in high school and college

Watching living cells through a microscope is much more exciting than seeing pictures of cells in high school and college textbooks. However, bringing cell cultures into the classroom is challenging for biology teachers since culturing cells requires sophisticated and expensive instruments such as a CO2 incubator and an inverted phase-contrast microscope. Here, we describe easy and affordable methods to culture and observe skeletal muscle cells using the L-15 culture medium, tissue culture flask, standard dry incubator, standard upright microscope, and modified Smartphone microscope. Watching natural living cells in a “Do-It-Yourself (DIY)” way may inspire more students’ interest in cell biology.

Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch.

Hydrophobic mismatch between a lipid membrane and embedded transmembrane peptides or proteins plays a role in their lateral localization and function. Earlier studies have resolved numerous mechanisms through which the peptides and membrane proteins adapt to mismatch, yet the energetics of lateral sorting due to hydrophobic mismatch have remained elusive due to the lack of suitable computational or experimental protocols. Here, we pioneer a molecular dynamics simulation approach to study the sorting of peptides along a membrane thickness gradient. Peptides of different lengths tilt and diffuse along the membrane to eliminate mismatch with a rate directly proportional to the magnitude of mismatch. We extract the 2-dimensional free energy profiles as a function of local thickness and peptide orientation, revealing the relative contributions of sorting and tilting, and suggesting their thermally accessible regimes. Our approach can readily be applied to study other membrane systems of biological interest where hydrophobic mismatch, or membrane thickness in general, plays a role.

A Microwave‐Assisted One‐Pot Three‐Step Metal‐Free [4+2] Annulation for the Sustainable Synthesis of Highly Substituted 1,2,4‐Triazines

AbstractHerein we report the first microwave‐assisted one‐pot three‐step metal‐free [4+2] procedure for the synthesis of 5,6‐substituted‐3‐hydrazinyl‐1,2,4‐triazines directly from commercially available aromatic and heteroaromatic ketones. The 3‐hydrazinyl‐1,2,4‐triazine can be isolated or further elaborated, after a simple work‐up, by direct condensation with different aldehydes or ketones to provide highly functionalized hydrazone‐derivatives. This protocol represents a rapid, efficient, and sustainable approach for the development of new highly functionalized 1,2,4‐triazine derivatives with potential biological interest.