Genetic Theory Research Articles

Human Facts, Collective Subjects and Author's Worldview in Pendekar Cengeng Silat Story by Kho Ping Hoo

This research explains the relations and implications of Kho Ping Hoo's discrimination experiences as a Peranakan Tionghoa group to the emergence of the Pendekar Cengeng silat story . Data were collected using reading and note-taking techniques. Data were analyzed using Lucien Goldmann's genetic structuralism theory which focuses on human facts, collective subjects, and the author's worldview. The research results show that human facts include various activities carried out by warrior figures in an effort to oppose the oppression of the colonial government. The collective subject shows a group of warriors who work together and are united in one group to carry out the warrior's mission collectively. The author's worldview are about politics, religiosity and life philosophy.

Plant Breeding and the Origins of Genetics.

This paper argues that the historiography of genetics ∼1900, the formation period of modern science, is too narrow. It lacks attention to plant breeding. Perhaps this omission also narrows the present understanding of fundamental ideas like the genotype/phenotype distinction and the gene concept? There is a mythical story still told in textbooks and at anniversaries: As modern genetics started with the rediscovery of Mendel's laws in 1900, a fateful controversy over continuous or discontinuous variation of heredity between biometricians and Mendelians. Discontinuity appeared as a threat to the Darwinian theory of evolution by natural selection. Only by the 1920s was the problem solved by a theory of population genetics founded on the chromosome theory of heredity.1 However, in plant breeding ∼1900 ideas of heredity and evolution were closely intertwined, and the combination of discontinuous heredity with continuous Darwinian evolution was an obvious option.

Two fitness inference schemes compared using allele frequencies from 1068 391 sequences sampled in the UK during the COVID-19 pandemic

Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population genetics theory but with different assumptions. One approach, tQLE, features an epistatic fitness landscape and assumes that alleles are nearly in linkage equilibrium. Another approach, MPL, assumes a simple, additive fitness landscape, but allows for any level of correlation between alleles. We characterized differences in the distributions of fitness values inferred by each approach and in the ranks of fitness values that they assign to sequences across time. We find that in a large fraction of weeks the two methods are in good agreement as to their top-ranked sequences, i.e. as to which sequences observed that week are most fit. We also find that agreement between the ranking of sequences varies with genetic unimodality in the population in a given week.

Forward and backward modeling of cultural evolutionary processes

Modern cultural evolution theory adopts a variety of concepts and methods developed in mathematical biology, in particular population genetics theory. In addition to forward-looking approaches such as two-locus models, backward-looking approaches such as coalescent theory, which describe ancestral states of the current population, have played an important role in population genetics. Here, we show how forward and backward approaches can be applied to two examples in cultural evolution. The first example deals with the number of cultural traits, which can be analyzed by a backward approach. Cultural coalescent theory illustrates many unique aspects of cultural processes such as information transfer (i.e., social learning) from many donors ("cultural parents"), including or excluding the biological parents. Theory predicts that many cultural traits of intermediate (or higher) frequency (popularity) can exist that are surprisingly old. Many unsolved issues remain, however, such as how to incorporate social structure as well as natural and/or cultural selection, which we believe to be an urgent agenda. The second example is the punishment of sibling incest, a problem to which cultural coalescent theory cannot currently be usefully applied. By analyzing forward recursions, we show that punishment is ineffective in suppressing incest, unless the incestuous inclination is diminished by the presence of punishers. Based on these examples, we discuss the merits and demerits of forward and backward approaches.

Perspectives on Ergodic Cancer Therapy Derived from Cloning Genome Chaos via In Vivo Rhabdomyosarcoma RA-2 Models: a Narrative Review.

This review explores articles concerning the experimental research cycle on genome instability in cell populations of highly malignant recurrent organotropic rhabdomyosarcoma RA- 2 in rats. Clonal analysis and cloning were pivotal components of this research, which relies on the frequency of cells with micronuclei and internuclear bridges to gauge the intensity of chromothripsis and break-fusion-bridge cycles. The efficacy of cloning, determined by these indicators, stemmed from the deliberate isolation of tumor stem cells, yielding clones in which chromothripsis activity and breakage-fusion-bridge cycles were sustained. Notably, it is plausible that the stem cells themselves, progenitors of these clones, harbor dicentric chromosomes and chromosomal fragments, contributing to the formation of "fatal micronuclei" in their karyotype. Cloning based on bridges and micronuclei has proven effective up to a certain threshold (15%-18%), reaffirming the predicted reproductive extinction of malignant cell populations under mutational pressure and genome chaos, as posited by the genetic theory of cell populations. Furthermore, this review highlights the potential of ergodic cancer therapy as a novel therapeutic strategy. Ergodic therapy offers promising prospects for late-stage and terminal malignant tumors, where conventional treatments may fall short due to advanced progression. Furthermore, by "enhancing chromothripsis" through the induction of additional micronuclei and bridges, ergodic cancer therapy seeks to increase genome chaos to a critical threshold, potentially halting malignant progression. This innovative approach presents opportunities to explore new drugs and targets for chromothripsis-based oncotherapy, addressing the pressing need for effective treatments in advanced stages of malignancy.

Genetic Insights and Epidemiological Models in Understanding Primary Open Angle Glaucoma

Primary open-angle glaucoma (POAG) is a multifactorial chronic optic neuropathy with significant genetic heterogeneity. The pathogenesis of POAG involves an imbalance between the production and drainage of aqueous humor (AH). Genetic theories suggest that transgenic mice demonstrating the GLU50LYS mutation in optineurin (OPTN) experience retinal ganglion cell apoptosis, while mutant myocilin (MYOC) proteins induce endoplasmic reticulum (ER) stress, leading to an unfolded protein response (UPR) and subsequent apoptosis of trabecular meshwork cells (TMC). Furthermore, the interaction between MYOC and mitochondria in the trabecular meshwork (TM) and astrocytes may lead to mitochondrial membrane depolarization and calcium channel dysregulation, contributing to POAG. Overexpression of MYOC variants (P370L, Q368X) is also implicated, as are epigenetic modifications and signaling pathways such as histone and DNA modification. POAG has been associated with autosomal dominant inheritance, with mutations in MYOC and OPTN being prominent causative factors, although many cases involve multiple genetic loci. Currently, over 20 genetic loci have been linked to POAG, with 14 chromosomal loci (GLC1A to GLC1N) identified, 5 of which contribute to juvenile-onset open-angle glaucoma (JOAG). Of these loci, MYOC, OPTN, WD repeat domain 36 (WDR36), and neurotrophin-4 (NTF4) are the most studied causative genes. The ongoing study of molecular genetics offers potential pathways for future therapeutic advances in the treatment of POAG.

Design and practice of educational experiments on genetic epistasis.

Genetic epistasis is a fundamental concept in genetics that describes how interactions between genes determine phenotypic traits. To enhance students' understanding and practical application of genetic epistasis, this experiment is designed and conducted using gene mutations in the adenine biosynthesis pathway of Saccharomyces cerevisiae (baker's yeast). S. cerevisiae is a classic model organism for genetic teaching experiments. In its adenine biosynthesis pathway, a mutation in the ADE2 gene leads to the accumulation of the intermediate 5'-phosphoribosylaminoimidazole (AIR), causing the cells to appear red. However, if a gene upstream of ADE2 in the adenine biosynthesis pathway (such as ADE8) is defective, the red phenotype of yeast will disappear. Conversely, a defect in a gene downstream of ADE2 (such as ADE1) does not alter the red phenotype. Therefore, ADE8 is epistatic to ADE2. In this experiment, the CRISPR-Cas9 genome editing technology is employed, allowing students to perform single knockout of ade2Δ, as well as double knockouts of ade2Δade8Δ and ade2Δade1Δ in S. cerevisiae. By observing the phenotypic changes in yeast mutants from white to red and back to white, students gain a profound understanding of the basic genetic theory of how genes determine phenotypes and the concept of epistasis in gene interactions. This experiment also enables students to master fundamental yeast genetic techniques, significantly enhancing their ability to design and conduct experiments in real research environments. This is of great significance for their future research work and academic development.

Dominance reversal protects large-effect resistance polymorphisms in temporally varying environments.

A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation in heterogeneous environments 1,2 . Population genetics theory suggests that beneficial reversal of dominance, where alleles are dominant when beneficial and recessive when deleterious, can help maintain such variation in temporally varying environments 3,4 . However, empirical examples are scarce 5 due to difficulties in measuring dominance in fitness in field experiments 6 . Here we quantify the selective effects and dominance of large-effect insecticide-resistant alleles at the Ace enzymatic locus in Drosophila melanogaster 7 . In laboratory assays, we identify a beneficial reversal of dominance of the Ace alleles for fitness-associated phenotypes under selection in the presence and absence of malathion, a widely used organophosphate insecticide. Using highly replicated field mesocosms, we show that resistant Ace alleles fluctuate rapidly in response to a pulse of malathion, but are maintained in its absence. We show that this pattern is only consistent with beneficial reversal of dominance, where the resistant Ace alleles are dominant and beneficial for resistance and recessive and deleterious for enzymatic function. Moreover, we find that seasonally fluctuating selection due to insecticide resistance can generate fluctuating chromosome-scale genomic perturbations of allele frequencies. We propose an extension to Wright's physiological theory of dominance 8 , arguing that under fluctuating selection the currently deleterious allele should often behave as loss-of-function and thus recessive to the currently beneficial allele. Overall, our results suggest that beneficial reversals of dominance can be common and can help both maintain genetic variation and allow for rapid evolutionary responses to environmental shifts.

Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.

Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends.

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations' Global Biodiversity Framework (GBF). However, there is a lack of reliable large-scale predictive frameworks to quantify how much genetic diversity has already been lost, let alone to quantitatively predict future losses under different conservation scenarios in the 21st century. Combining spatio-temporal population genetic theory with population genomic data of 18 plant and animal species, we studied the dynamics of genetic diversity after habitat area losses. We show genetic diversity reacts slowly to habitat area and population declines, but lagged losses will continue for many decades even after habitats are fully protected. To understand the magnitude of this problem, we combined our predictive method with species' habitat area and population monitoring reported in the Living Planet Index, the Red List, and new GBF indicators. We then project genetic diversity loss in 13,808 species with a short-term genetic diversity loss of 13-22% and long-term loss of 42-48% with substantial deviations depending on the level of habitat fragmentation. These results highlight that protection of only current habitats is insufficient to ensure the genetic health of species and that continuous genetic monitoring alone likely underestimates long term impacts. We provide an area-based spatio-temporal predictive framework to develop quantitative scenarios of global genetic biodiversity.

Understanding admixture fractions: theory and estimation of gene-flow.

Estimation of admixture proportions has become one of the most commonly used computational tools in population genomics. However, there is remarkably little population genetic theory on statistical properties of these variables. We develop theoretical results that can accurately predict means and variances of admixture proportions within a population using models with recombination and genetic drift. Based on established theory on measures of multilocus disequilibrium, we show that there is a set of recurrence relations that can be used to derive expectations for higher moments of the admixture proportions distribution. We obtain closed form solutions for some special cases. Using these results, we develop a method for estimating admixture parameters from estimated admixture proportions obtained from programs such as Structure or Admixture. We apply this method to HapMap 3 data and find that the population history of African Americans, as expected, is not best explained by a single admixture event between people of European and African ancestry. The model of constant gene flow starting at 8 generations and ending at 2 generations before present gives the best fit.

Predictability and evolutionary determinism — the search for quantitative explanation

Physics describes reality through the understanding and elucidation of physical laws. From these laws, the universe is predictable. It has indeed been suggested that explanation of observable phenomena comes from our ability to predict these events, through our understanding of physical laws and causal processes. Biological entities operate, of course, through physical and chemical laws. But there exist biological processes that have emergent properties, notably the evolution of adaptation through natural selection, which add an extra dimension to the concept of the understanding of biological phenotypes. The population genetic theory of evolution is mathematically formulated, and contains elements of determinism, typified by the action of natural selection, and elements of randomness, typified by the action of genetic drift and by the randomness of mutation. But is the goal-directed property of natural selection sufficient to conclude that the deterministic elements of the evolutionary process make evolutionary change predictable? And to what extent can we expect 'adaptation' to function as an explanation of biological phenotypes?

IMPRS 2024: Interdisciplinary Approaches to the Foundations of Human Speech

The International Max Planck Research School (IMPRS) biennial conference on psycholinguistics focused on the psychological, social, and biological foundations of human speech. The conference took an interdisciplinary approach, drawing on data from cognitive research, neuroscience, computer science, medicine, genetics, anthropology, and evolutionary theory. This article provides an overview of the keynote speeches and the most significant posters, presenting the findings of scholars from around the world.

346 Investigating the potential of incorporating indirect genetic effects into genetic evaluations of dairy calf disease traits

Abstract The goal of infectious disease control is often local eradication, but this is theoretically impossible to achieve based on classical quantitative genetic theory. Current methods focus on the susceptibility of individuals to disease and assume that exposure to a pathogen is 1) constant over time, 2) equal among individuals, and (3) due entirely to the environment. For this reason, it is likely that conventional genetic methods are capturing only a fraction of genetic variation in disease occurrence. The incorporation of epidemiological theory into quantitative genetics provides an opportunity to better determine the level of genetic variation in infectious disease traits. This stems from the ability to include the positive feed-back dynamics of infectious disease transmission. From an epidemiolocal perspective, both susceptibility and infectivity also have indirect genetic effects (IGE), because the genotype of one individual impacts the risk of infection of other individuals, and this can drastically affect the rate and direction of response to selection. Epidemiological models unravel the genetic heterogeneity in both susceptibility and infectivity traits, and account for the impact each animal has on its contemporaries compared with conventional quantitative genetic approaches. From a calf health perspective, there is a shift towards group housing dairy calves, primarily due to welfare and social acceptability. In turn, this will lead to increased animal interactions from a young age. Therefore, the aim of this study was to investigate the potential of incorporating IGE into current quantitative approaches to determine its impact on selection potential. Our study looked at two common infectious diseases in calves on dairy farms: respiratory problems (RESP) and diarrhea (DIAR). Producer-recorded data comprised of 19,445 records collected on 34 herds that group housed calves between 2007 and 2020. Calves were allocated into pen groups based on birth dates and herd specific housing practices. Original phenotypes were split into 10 records, each representing a week of life, to determine when exactly calves became sick and infective. Several scenarios were investigated with respect to the time an animal was infective for following a disease case (1 or 2 wk), and the maximum difference in weeks between animal birth dates to be included within the same pen (2 to 5 wk). Variance components were estimated using a generalized linear mixed model fitting a complementary-log-log link function with offset for exposure. Initial heritability estimates for susceptibility on the observed scale for DIAR ranged from 0.03 to 0.07, and from 0.02 to 0.03 for RESP across scenarios. While heritability estimates for infectivity are currently being investigated, the results for susceptibility highlight the potential for incorporating IGE into genetic evaluation of disease traits and provide an introduction towards incorporating epidemiological theory into classical quantitative approaches to better respect the transmission dynamics of infections.

Insights into the genetic theory of infectious diseases.

Over the past century, classical approaches from microbiology and immunology have produced spectacular results in the control of infectious diseases. However, the recent SARS-COV-2 pandemic has highlighted our continued failure to control some infections. Other microorganisms still pose a threat to humanity such as HIV, Ebola, and influenza viruses. It seems that conventional approaches are not able to solve all the current problems caused by infectious diseases. Human genetics has shown that infections have a strong genetic determinism that can lead to a predisposition or resistance to infections. This explains much of the clinical variability observed in individuals infected with the same pathogen. The identification of the genetic etiology allows a better understanding of the pathogenesis of infectious diseases and, consequently, the consideration of appropriate preventive and therapeutic strategies. This review provides insights into the genetic theory and the concrete evidence to support it. We highlight the role of primary immunodeficiencies in the discovery of Mendelian and monogenic susceptibility to infections, then we show how genetic and phenotypic heterogeneity, redundancy, and resistance to infection manifest in the context of this genetic determinism. To effectively combat the constant threat of microbes, it is essential to integrate human genetics with microbiology to examine the interactions between pathogens and our immune system.

Sosialisasi Bahaya Narkotika sebagai Bentuk Kenakalan Remaja di kalangan Siswa SMKN 1 Kecamatan Kragilan Kabupaten Serang

Narcotics are a substance that is very dangerous if its use is misused and permission is not obtained from the authorities, narcotics will damage the nation's next generation who will run the government in the future. The rise in the use of narcotics is in line with the influx of globalization and modernization which makes it easier for people to obtain them as well as a network of dealers who are aggressively looking for marketing targets among young people who are susceptible to sweet advances and do not yet have clear life principles. Indonesia is one of the countries that is fighting drug dealers, users and networks, this is because every 17 seconds someone is arrested for violating drug-related laws. Indonesia has 2 laws that regulate the misuse of narcotics, namely Law No. 35 of 2009 and Law No. 5 of 1997. All of them are clear about the sanctions and dangers of using narcotics, the punishment can even be death. This service journal refers to biological theory which explains the biological theory of the brain, metabolic imbalance theory, and genetic theory. Many experts, especially biological experts, say that narcotics will damage brain growth and development. This service journal uses literature and seminar methods which are expected to provide an explanation of a situation where an individual or person will have a bleak future if they fall into the use of narcotics because it will damage brain tissue and damage the body. As early as possible, we will unite together to fight against narcotics, not only for law officers who work, but all elements of society are involved in fighting the use of narcotics which has penetrated young people, especially among teenagers who are still at school, who are vulnerable to the temptation of using narcotics.

PopDMS infers mutation effects from deep mutational scanning data.

Deep mutational scanning (DMS) experiments provide a powerful method to measure the functional effects of genetic mutations at massive scales. However, the data generated from these experiments can be difficult to analyze, with significant variation between experimental replicates. To overcome this challenge, we developed popDMS, a computational method based on population genetics theory, to infer the functional effects of mutations from DMS data. Through extensive tests, we found that the functional effects of single mutations and epistasis inferred by popDMS are highly consistent across replicates, comparing favorably with existing methods. Our approach is flexible and can be widely applied to DMS data that includes multiple time points, multiple replicates, and different experimental conditions. popDMS is implemented in Python and Julia, and is freely available on GitHub at https://github.com/bartonlab/popDMS.

Understanding the Multifaceted Process of Aging: Theories, Mechanisms, and Implications for Treatment

The aging process is a multifaceted biological phenomenon characterized by alterations at the molecular, cellular, and organ levels that culminate in a gradual, unavoidable, and unavoidable reduction in the body's capacity to react suitably to internal and/or external stimuli. Aging is a complex process that involves different mechanisms as The "Wear and Tear" Theory ,The Genetic Control Theory ,The Neuroendocrine Theory ,Waste Accumulation Theory ,Divisions Theory, Autoimmune Theory, Thymic-Stimulating Theory ,Mitochondrial Theory Mitochondria, Errors and Repairs Theory, Redundant DNA Theory Cross-Linkage Theory , Death Hormone Theory (DECO), Caloric Restriction Theory ,The Rate of Living Theory ,Gene Mutation Theory, Accumulated mutations Theory, Theory, Order to Disorder Theory, Disposable soma Theory, Antagonistic pleiotropy theory, The Telomerase Theory ,The free radical Theory. The two main categories of aging theories that explain cellular aging are structural damage and programmed theories. Different types of cells experience physiological stressors due to a range of circumstances. Notably, post-mitotic and mitotic cells have different capacities for proliferation and age differently in response to these pressures through different processes of cellular senescence and death, respectively. Over time, these aging cells build up and eventually cause old tissues to malfunction. The aim of this review is to throw light upon the effected of aging and who to treatment it.

Study the structure, stability and CO2 adsorption of the ScVB5 cluster

A combination of genetic algorithm and density functional theory (GA-DFT) was used to calculate the minimum structures of ScVB5 clusters. The thirteen isomers of ScVB5 cluster were investigated at the level of PBE/def2-TZVPP, TPSSh/def2-TZVPP, and TPSSh/def2-QZVP levels. The relative energies, the structural geometry, ionization energy, affinity energy of neutral isomers were reported. The ScVB5 cluster can be formed by adding atom into smaller clusters. The proposed structure of ScVB5 cluster for CO2 treatment is a pentagonal bipyramid in the Cs symmetry with vanadium atom at one of the vertices and scandium atom in the base of bipyramid. The favor position for adsorp CO2 by the ScVB5 cluster were at around of Sc and V atoms. The dual transition metal-doped boron clusters can interact with CO2 molecules stronger than pure boron clusters.

Genetic Factors Contributing to Respiratory Disorders in Brachycephalic Dog Breeds in Uganda

Purpose: To aim of the study was to analyze the genetic factors contributing to respiratory disorders in brachycephalic dog breeds. Methodology: This study adopted a desk methodology. A desk study research design is commonly known as secondary data collection. This is basically collecting data from existing resources preferably because of its low cost advantage as compared to a field research. Our current study looked into already published studies and reports as the data was easily accessed through online journals and libraries. Findings: Genetic factors are primary contributors to respiratory disorders in brachycephalic dog breeds, known for their flattened facial structure. Breeds like Bulldogs and Pugs exhibit narrowed nostrils, elongated soft palates, and other airway obstructions due to selective breeding for these distinctive traits. These anatomical abnormalities restrict airflow, leading to symptoms such as noisy breathing and exercise intolerance. Unique Contribution to Theory, Practice and Policy: Genetic inheritance theory, evolutionary genetics theory & genotype-environment interaction theory may be used to anchor future studies on genetic factors contributing to respiratory disorders in brachycephalic dog breeds. Implement breeding programs that prioritize genetic health over physical appearance. Establish and enforce regulatory standards for breeding brachycephalic dogs that include mandatory genetic testing for respiratory disorder markers.