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Among the offspring of humans and other animals are occasional individuals that are malformed in whole or in part. The most grossly abnormal of these have been referred to from ancient times as monsters, because their birth was thought to foretell doom; the less severely affected are usually known as anomalies. This volume digs deeply into the cellular and molecular processes of embryonic development that go awry in such exceptional situations. It focuses on the physical mechanisms of how genes instruct cells to build anatomy, as well as the underlying forces of evolution that shaped these mechanisms over eons of geologic time. The narrative is framed in a historical perspective that should help students trying to make sense of these complex subjects. Each chapter is written in the style of a Sherlock Holmes story, starting with the clues and ending with a solution to the mystery.
Redroot pigweed (Amaranthus retroflexus L.) is a dominant weed in soybean [Glycine max (L.) Merr.] fields in Heilongjiang Province, China. High selective pressure caused by the extensive application of the protoporphyrinogen oxidase (PPO)-inhibiting herbicide fomesafen has caused A. retroflexus to evolve resistance to this herbicide. Two susceptible and two resistant populations (S1, S2, R1, and R2) were selected in this study to illustrate the target-site resistance mechanism in resistant A. retroflexus. Whole-plant bioassays indicated that R1 and R2 had evolved high-level resistance to fomesafen, with resistance factors of 27.0 to 27.9. Sequence alignment of the PPO gene showed an Arg-128-Gly substitution in PPX2. The basal expression differences of PPX1 and PPX2 between the S1 and R1 plants were essentially nonsignificant, whereas the basal expression of PPX2 in R2 plants was slightly lower than in S1 plants. Compared with the PPX1 gene, the PPX2 gene maintained higher expression in the resistant plants after treatment with fomesafen. An enzyme-linked immunosorbent assay showed a similar basal PPO content between the susceptible and resistant plants without treatment. After fomesafen treatment, the PPO content decreased sharply in the susceptible plants compared with the resistant plants. Furthermore, after 24 h of treatment, the resistant plants showed increased PPO content, whereas the susceptible plants had died. The PPO2 mutation resulted in high extractable PPO activity and low sensitivity to fomesafen along with changes in PPO enzyme kinetics. Although the mutant PPO2 exhibited increased Km values in the resistant plants, the Vmax values in these plants were also increased. Changes in the properties of the PPO enzyme due to an Arg-128-Gly substitution in PPX2, including changes in enzyme sensitivity and enzyme kinetics, are the target-site mechanism of resistance in A. retroflexus.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused acute respiratory distress syndrome affecting more than 200 countries with varied mortality rate. Successive genetic variants of SARS-CoV-2 become evident across the globe immediately after its complete genome sequencing. Here, we found a decent association of SARS-CoV-2 ORF3a mutation with higher mortality rate. Extensive in silico studies revealed several amino acid changes in ORF3a protein which ultimately leads to diverse structural modifications like B cell epitope loss, gain/loss of phosphorylation site and loss of leucine zipper motif. We could further relate these changes to the enhanced antigenic diversity of SARS-CoV-2. Through protein−protein network analysis and functional annotation studies, we obtained a close federation of ORF3a protein with host immune response via divergent signal transduction pathways including JAK-STAT, chemokine and cytokine-related pathways. Our data not only unveil the fairly appreciable association of ORF3a mutation with higher mortality rate, but also suggest a potential mechanistic insight towards the immunopathogenic manifestation of SARS-CoV-2 infection.
Here, I examine the shape of the tree of life on Earth that is the result of four billion years of birth, death, reproduction, and relatedness. This extended family tree has been produced by four billion years of using energy from the environment to power biological systems. I then consider the question of how to define life, from both evolutionary and metabolic perspectives. Defining life is not easy, but it is possible if we accept that viruses constitute a grey area. Next, I deal with the main driver of evolution on Earth (and probably elsewhere), namely Darwinian natural selection. This driver only works when there is variation among organisms, so our next port of call is how variation arises – gene mutation and related processes. Finally, I examine the origin of life. The emphasis here is on the hypothesis that life arose here rather than arriving pre-formed from another planet – the Terraspermia hypothesis. The alternative Panspermia hypothesis is considered to be fatally flawed.
Autism spectrum disorder (ASD) is a common neurodevelopmental disorder characterized by deficits in social communication and presence of restricted, repetitive behaviors, and interests. However, individuals with ASD vary significantly in their challenges and abilities in these and other developmental domains. Gene discovery in ASD has accelerated in the past decade, and genetic subtyping has yielded preliminary evidence of utility in parsing phenotypic heterogeneity through genomic subtypes. Recent advances in transcriptomics have provided additional dimensions with which to refine genetic subtyping efforts. In the current study, we investigate phenotypic differences among transcriptional subtypes defined by neurobiological spatiotemporal co-expression patterns. Of the four transcriptional subtypes examined, participants with mutations to genes typically expressed highly in all brain regions prenatally, and those with differential postnatal cerebellar expression relative to other brain regions, showed lower cognitive and adaptive skills, higher severity of social communication deficits, and later acquisition of speech and motor milestones, compared to those with mutations to genes highly expressed during the postnatal period across brain regions. These findings suggest higher-order characterization of genetic subtypes based on neurobiological expression patterns may be a promising approach to parsing phenotypic heterogeneity among those with ASD and related neurodevelopmental disorders.
The poorly understood aetiology of schizophrenia is known to involve a major genetic contribution even though the genetic factors remain elusive. Most genetic studies are based on Mendelian rules and focus on the nuclear genome, but current studies indicate that other genetic mechanisms are probably involved. This review focuses on mitochondrial DNA (mtDNA), a maternally inherited, 16.6-Kb molecule crucial for energy production that is implicated in numerous human traits and disorders. The aim of this review is to summarise the studies that have explored mtDNA in schizophrenia patients and those which provide evidence for its implication in this illness. Alterations in mitochondrial morphometry, brain energy metabolism, and enzymatic activity in the mitochondrial respiratory chain suggest a mitochondrial dysfunction in schizophrenia that could be related to the genetic characteristics of mtDNA. Moreover, evidence of maternal inheritance and the presence of schizophrenia symptoms in patients suffering from a mitochondrial disorder related to an mtDNA mutation suggest that mtDNA is involved in schizophrenia. The association of specific variants has been reported at the molecular level; however, additional studies are needed to determine whether the mitochondrial genome is involved in schizophrenia.
Common lambsquarters (Chenopodium album L.) is one of the most troublesome weeds in soybean [Glycine max (L.) Merr.] and corn (Zea mays L.) fields in northeast China. In 2017, a C. album population that survived imazethapyr at the recommended field rate was collected from a soybean field in Heilongjiang Province in China. Experiments were conducted to determine the basis of resistance to imazethapyr and investigate the herbicide-resistance pattern in C. album. Dose–response tests showed that the resistant population (R) displayed high resistance to imazethapyr (20-fold) compared with the susceptible population (S). An in vitro acetolactate synthase (ALS) activity assay indicated that the ALS of the R population was resistant to imazethapyr compared with the ALS of the S population. Sequence analysis of the ALS gene revealed that the GCA was replaced by ACA at amino acid position 122, which resulted in an alanine to threonine substitution (Ala-122-Thr) in the R population. The R population displayed cross-resistance to thifensulfuron-methyl and flumetsulam but susceptibility to bispyribac-sodium, flucarbazone, glyphosate, mesotrione, and fomesafen. These results confirmed that the basis of imazethapyr resistance in C. album was conferred by the Ala-122-Thr substitution in the ALS enzyme. This is the first report of the target-site basis of ALS-inhibiting herbicide resistance in C. album.
Chapter 5 deals with the genetics and cytogenetics of reproduction, starting again from asexual reproduction. Genetic variation due to new mutations, recombination, stochastic segregation or epigenetic causes is discussed. Moving to sexual reproduction, we discuss mechanisms of genetic exchange in the prokaryotes, but eventually focus more closely on sexual reproduction in the eukaryotes. First, the various sources of genetic variation (independent assortment of chromosomes and chromatids, crossing over and gene conversion at meiosis, syngamy) are discussed, thus addressing the genetics of hereditary transmission through different modes of sexual reproduction (amphigony, self-fertilization, meiotic and ameiotic parthenogenesis, gynogenesis, hybridogenesis, androgenesis). The last paragraphs of this chapter are devoted to sexual leakage and some special cases of sex in eukaryotes (conjugation in ciliates, parasexual cycle in fungi, chimerism).
Approximation sequences and derived equivalences occur frequently in the research of mutation of tilting objects in representation theory, algebraic geometry and noncommutative geometry. In this paper, we introduce symmetric approximation sequences in additive categories and weakly n-angulated categories which include (higher) Auslander-Reiten sequences (triangles) and mutation sequences in algebra and geometry, and show that such sequences always give rise to derived equivalences between the quotient rings of endomorphism rings of objects in the sequences modulo some ghost and coghost ideals.
Catchweed bedstraw (Galium aparine L.) is a problematic dicot weed that occurs in major winter wheat (Triticum aestivum L.) fields in China. Tribenuron-methyl has been widely used to control broadleaf weeds since 1988 in China. However, overuse has led to the resistance evolution of G. aparine to tribenuron-methyl. In this study, 20 G. aparine populations collected from Shandong and Henan provinces were used to determine tribenuron-methyl resistance and target-site resistance mechanisms. In dose–response experiments, 12 G. aparine populations showed different resistance levels (2.92 to 842.41-fold) to tribenuron-methyl compared with the susceptible population. Five different acetolactate synthase (ALS) mutations (Pro-197-Leu, Pro-197-Ser, Pro-197-His, Asp-376-Glu, and Trp-574-Leu) were detected in different resistant populations. Individuals heterozygous for Pro-197-Ser and Trp-574-Leu mutations were also observed in a resistant population (HN6). In addition, pHB4 (Pro-197-Ser), pHB7 (Pro-197-His), pHB8 (Pro-197-Leu), pHB5 (Asp-376-Glu), and pHB3 (Trp-574-Leu) subpopulations individually homozygous for specific ALS mutations were generated to evaluate the cross-resistance to ALS-inhibiting herbicides. The pHB4, pHB7, pHB8, pHB5, and pHB3 subpopulations all were resistant to sulfonylurea, pyrazosulfuron-ethyl, triazolopyrimidine, flumetsulam, sulfonylamino-carbonyl-triazolinone, flucarbazone-sodium, pyrimidinyl thiobenzoate, pyribenzoxim, and the imidazolinone imazethapyr. These results indicated the diversity of the resistance-conferring ALS mutations in G. aparine, and all these mutations resulted in broad cross-resistance to five kinds of ALS-inhibiting herbicides.
Recent progress in microdissection and in DNA sequencing has facilitated the subsampling of multi-focal cancers in organs such as the liver in several hundred spots, helping to determine the pattern of mutations in each of these spots. This has led to the construction of genealogies of the primary, secondary, tertiary, and so forth, foci of the tumor. These studies have led to diverse conclusions concerning the Darwinian (selective) or neutral evolution in cancer. Mathematical models of the development of multi-focal tumors have been devised to support these claims. We offer a model for the development of a multi-focal tumor: it is a mathematically rigorous refinement of a model of Ling et al. (2015). Guided by numerical studies and simulations, we show that the rigorous model, in the form of an infinite-type branching process, displays distributions of tumor size which have heavy tails and moments that become infinite in finite time. To demonstrate these points, we obtain bounds on the tails of the distributions of the process and an infinite series expansion for the first moments. In addition to its inherent mathematical interest, the model is corroborated by recent literature on apparent super-exponential growth in cancer metastases.
Recently, several incidents of glyphosate failure on junglerice [Echinochloa colona (L.) Link] have been reported in the midsouthern United States, specifically in Mississippi and Tennessee. Research was conducted to measure the magnitude of glyphosate resistance and to determine the mechanism(s) of resistance to glyphosate in E. colona populations from Mississippi and Tennessee. ED50 (dose required to reduce plant growth by 50%) values for a resistant MSGR4 biotype, a resistant TNGR population, and a known susceptible MSGS population were 0.8, 1.62, and 0.23 kg ae ha−1 of glyphosate, respectively. The resistance index calculated from the these ED50 values indicated that the MSGR4 biotype and TNGR population were 4- and 7-fold, respectively, resistant to glyphosate relative to the MSGS population. The absorption patterns of [14C]glyphosate in the TNGR and MSGS populations were similar. However, the MSGS population translocated 13% more [14C]glyphosate out of the treated leaf compared with the TNGR population at 48 h after treatment. EPSPS gene sequence analyses of TNGR E. colona indicated no evidence of any point mutations, but several resistant biotypes, including MSGR4, possessed a single-nucleotide substitution of T for C at codon 106 position, resulting in a proline-to-serine substitution (CCA to TCA). Results from quantitative polymerase chain reaction analyses suggested that there was no amplification of the EPSPS gene in the resistant populations and biotypes. Thus, the mechanism of resistance in the MSGR population (and associated biotypes) is, in part, due to a target-site mutation at the 106 loci of the EPSPS gene, while reduced translocation of glyphosate was found to confer glyphosate resistance in the TNGR population.
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices in each of its clusters and by preserving connections between them. (Here, by cluster, we mean a maximal connected component of the forest in which all vertices have the same type.) We first show that the forest of mutations of any multitype branching forest is itself a branching forest. Then we give its progeny distribution and we describe some of its crucial properties in terms of the initial progeny distribution. We also obtain the limiting behaviour of the number of mutations both when the total number of individuals tends to ∞ and when the number of roots tends to ∞. The continuous-time case is then investigated by considering multitype branching forests with edge lengths. When mutations are nonreversible, we give a representation of their emergence times which allows us to describe the asymptotic behaviour of the latter, under certain conditions on the mutation rates. These results have potential relevance for emergence of mutations in population cells, particularly for genetic evolution of cancer or development of infectious diseases.
Monitoring milk quality traits and the classification of raw milk are important steps for generating high-quality dairy products. Given the important roles of the BRG1/BRM-associated factor 60c (BAF60c) gene in the regulation of physiological growth and production, the objective of the current study was to analyse the association between the BAF60c gene and milk quality and establish a gene-based method for pre-evaluating raw milk quality. For this purpose, DNA was isolated from 507 milk samples and genotyped using the polymerase chain reaction-restricted fragment length polymorphism method. Milk quality traits including milk protein percentage (MPP), milk fat percentage (MFP), lactose percentage (LP) and total solids content (TSC) were also evaluated from the same 507 milk samples. The newly found 6060 T > C mutation of the BAF60c gene was associated significantly with MPP and LP, but not with MFP and TSC. The results demonstrated that this mutation could be used for the pre-evaluation of MPP and LP; therefore, raw milk could be graded according to different genotypes.
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 X-chromosome SNPs) on 383 female sheep. Genotype allele intensity values, either as their original raw values or transformed to logarithm intensity ratio (LRR), were used to accurately diagnose two dizygotic (i.e. fraternal) twin 53,X sheep, both of which received their single X chromosome from their sire. This is the first reported case of 53,X dizygotic twins in any species. Relative to the X-chromosome SNP genotype mean allele intensity values of normal females, the mean allele intensity value of SNP genotypes on the X chromosome of the two females monosomic for the X chromosome was 7.45 to 12.4 standard deviations less, and were easily detectable using either the AxiomTM or Illumina genotype platform; the next lowest mean allele intensity value of a female was 4.71 or 3.3 standard deviations less than the population mean depending on the platform used. Both 53,X females could also be detected based on the genotype LRR although this was more easily detectable when comparing the mean LRR of the X chromosome of each female to the mean LRR of their respective autosomes. On autopsy, the ovaries of the two sheep were small for their age and evidence of prior ovulation was not appreciated. In both sheep, the density of primordial follicles in the ovarian cortex was lower than normally found in ovine ovaries and primary follicle development was not observed. Mammary gland development was very limited. Results substantiate previous studies in other species that aneuploidy can be readily detected using SNP genotype allele intensity values generally already available, and the approach proposed in the present study was agnostic to genotype platform.
Italian ryegrass has invaded wheat ﬁelds in China and is becoming a predominant, troublesome weed. Fenoxaprop-P-ethyl has been widely used for weed control on Chinese farms since the 1990s. However, overuse has led to fenoxaprop-P-ethyl resistance in Italian ryegrass in Chinese wheat fields. In this study, we identified a putative fenoxaprop-P-ethyl–resistant population of Italian ryegrass, HZYC-6, from Henan province, China. Mutations involving Asp-2078-Gly and Ile-1781-Leu substitutions were identified in the carboxyl-transferase domain of acetyl-coenzyme A carboxylase in this population, and these mutations are the likely cause of the target site–based resistance to fenoxaprop-P-ethyl. In addition, we identified cytochrome P450–mediated metabolism of herbicides (non–target site based resistance) in the HZYC-6 population, indicating that multiple mechanisms of resistance may be segregating in this population. Furthermore, HZYC-6 was also highly resistant to haloxyfop-R-methyl and quizalofop-P-ethyl, moderately resistant to clodinafop-propargyl and sethoxydim, and had low resistance to clethodim and pinoxaden.
We consider a Yule process until the total population reaches size n ≫ 1, and assume that neutral mutations occur with high probability 1 - p (in the sense that each child is a new mutant with probability 1 - p, independently of the other children), where p = pn ≪ 1. We establish a general strategy for obtaining Poisson limit laws and a weak law of large numbers for the number of subpopulations exceeding a given size and apply this to some mutation regimes of particular interest. Finally, we give an application to subcritical Bernoulli bond percolation on random recursive trees with percolation parameter pn tending to 0.
Eclipta, widespread in tropical, subtropical, and temperate regions, is one of the main malignant broadleaf weeds and thrives in moist and dryland fields. Field rates of acetolactate synthase (ALS) inhibitors have failed to control eclipta in some farmlands in China. One ALS inhibitor–resistant population (R) collected from Jiangsu province in China was confirmed in the greenhouse in our preliminary work. Whole-plant assays revealed that this R population was highly resistant to four sulfonylureas (pyrazosulfuron-ethyl, 134-fold; bensulfuron-methyl, 172-fold; metsulfuron-methyl, 30-fold; and tribenuron-methyl, 195-fold), two triazolopyrimidines (pyroxsulam, 98-fold; penoxsulam, 30-fold), and one pyrimidinylthio-benzoate (bispyribac-sodium, 166-fold) and was moderately resistant to two imidazolinones (imazethapyr, 10-fold; imazapic, 19-fold). ALS enzyme-activity assays showed insensitivity of the ALS from the R population (resistance index values ranged from 12 to 293) to all of the above ALS inhibitors in vitro. Chromatograms from ALS gene sequence analysis detected a homozygous Pro-197-Ser amino acid substitution in the R population. These results confirmed that the Pro-197-Ser substitution results in broad-spectrum cross-resistance to ALS inhibitors in the eclipta R population. To our knowledge, this study is the first to report broad cross-resistance to ALS inhibitors in eclipta and to obtain the full-length ALS gene sequence.
Methiozolin is an isoxazoline herbicide being investigated for selective POST annual bluegrass control in managed turfgrass. Research was conducted to evaluate methiozolin efficacy for controlling two annual bluegrass phenotypes with target-site resistance to photosystem II (PSII) or enolpyruvylshikimate-3-phosphate synthase (EPSPS)-inhibiting herbicides (i.e., glyphosate), as well as phenotypes with multiple resistance to microtubule and EPSPS or PSII and acetolactate synthase (ALS)-inhibiting herbicides. All resistant phenotypes were established in glasshouse culture along with a known herbicide-susceptible control and treated with methiozolin at 0, 125, 250, 500, 1000, 2000, 4000, or 8000 g ai ha−1. Methiozolin effectively controlled annual bluegrass with target-site resistance to inhibitors of EPSPS, PSII, as well as multiple resistance to EPSPS and microtubule inhibitors. Methiozolin rates required to reduce aboveground biomass of these resistant phenotypes 50% (GR50 values) were not significantly different from the susceptible control, ranging from 159 to 421 g ha−1. A phenotype with target-site resistance to PSII and ALS inhibitors was less sensitive to methiozolin (GR50=862 g ha−1) than a susceptible phenotype (GR50=423 g ha−1). Our findings indicate that methiozolin is an effective option for controlling select annual bluegrass phenotypes with target-site resistance to several herbicides.
Although the birth of twins has always attracted attention, there are no known genetic or environmental factors that can determine the birth of monozygotic (MZ) twins. And even for dizygotic (DZ) twins, genetic influences are not completely understood. A previous study from our group has shown that the C allele of polymorphism rs1042522 in the TP53 gene was more frequent in the mothers of twins than in the mothers of singletons in a small village in South Brazil. In order to clarify whether this was an isolated factor, we performed a population-based, observational case-control study. Samples were selected from a state-funded program of paternity investigation. Samples were considered cases when two of the children had the same date of birth, whereas controls were those samples in which at least two children were born in different dates. The first subsequent sample fulfilling control criteria was included after each case. From 2007 to 2013, 32,661 records were searched and 283 (0.9%) twins were found (119 MZ and 164 DZ). Genotypic and allele frequencies were not different between mothers of twins or mothers of singletons. However, mothers of MZ twins showed a higher frequency of GG genotype and lower frequency of the C allele when compared to mothers of DZ twins. Also, the proportion of MZ twins (42%) was higher than usually reported (30%). Finally, the proportion of twins found in this study seems to be more realistic, as this sample was allegedly not from users of assisted reproduction techniques.