Divergent Class Research Articles

Application of a Cell-Free Synthetic Biology Platform for the Reconstitution of Teleocidin B and UK-2A Precursor Biosynthetic Pathways.

We report the successful cell-free reconstitution of two natural product biosynthetic pathways of divergent complexity and structural classes. We first constructed the teleocidin biosynthetic pathway using our BY-2 (tobacco) cell-free protein synthesis (CFPS) system. We discovered a direct interaction between TleA and MbtH, and showed that the BY-2 system is capable of producing more than 80 mg/L teleocidin B-3 with cofactor supplementation and ∼20 mg/L with no cofactors supplemented, demonstrating the high metabolic activity of the system. We then extended our methodology and report the first successful cell-free biosynthesis of UK-2 diol (precursor to the commercially valuable secondary metabolite UK-2A) from simple building blocks by refactoring a complex pathway of 10 proteins in the wheat germ CFPS system. We show that plant CFPS systems are suitable for reconstructing pathways and identifying the functions of uncharacterized genes linked to biosynthetic gene clusters and rate-limiting biosynthetic steps.

Sphingolipid homeostasis--how do cells know when enough is enough? Implications for plant pathogen responses.

Sphingolipid homeostatic regulation is important for balancing plant life and death. Plant cells finely tune sphingolipid biosynthesis to ensure sufficient levels to support growth through their basal functions as major components of endomembranes and the plasma membrane. Conversely, accumulation of sphingolipid biosynthetic intermediates, long-chain bases (LCBs) and ceramides, is associated with programmed cell death (PCD). Limiting these apoptotic intermediates is important for cell viability; while overriding homeostatic regulation permits cells to generate elevated LCBs and ceramides to respond to pathogens to elicit the hypersensitive response in plant immunity. Key to sphingolipid homeostasis is serine palmitoyltransferase (SPT), an ER-associated, multi-subunit enzyme catalyzing the first step in the biosynthesis of LCBs, the defining feature of sphingolipids. Across eukaryotes, SPT interaction with its negative regulator ORM is critical for sphingolipid biosynthesis. The recent cryo-electron microscopy structure of the Arabidopsis SPT complex indicates that ceramides bind ORMs to competitively inhibit SPT activity. This system provides a sensor for intracellular ceramide concentrations for sphingolipid homeostatic regulation. Combining the newly elucidated Arabidopsis SPT structure and mutant characterization, we present a model for the role of the two functionally divergent Arabidopsis ceramide synthase classes to produce ceramides that form repressive (trihydroxy LCB-ceramides) or non-repressive (dihydroxy LCB-ceramides) ORM interactions to influence SPT activity. We describe how sphingolipid biosynthesis is regulated by the interplay of ceramide synthases with ORM-SPT when "enough is enough" and override homeostatic suppression when "enough is not enough" to respond to environmental stimuli such as microbial pathogen attack.

A Comparative Study of China and U.S.: The Influence of Digital Divide on Education Inequality and Its Mitigating Policies

Under the digital age, the method of learning expanded to the virtual setting. With resources shared through online platforms, digital divide became a new problem in achieving education equality. This paper intends to examine the effect of digital divide on educational system in the U.S. and China from a comparative perspective. This study adopts literature review as its research method. Types of digital divide that occurs in the two countries showcase some similarities, yet the factors attributing to the educational digital divide varies widely. Educational divide exists in different social groups. Systematic and cultural differences are the root behind these factors. In the U.S., digital divide occurred due to differences at multiple levels: race, state, schools, and family SES. In China, digital divide occurs due to geological divergence, generational division, and social class. The root Moreover, mitigating policies from the two countries illustrate how the U.S. and China access the issue from different perspective. The root behind such contrast is the difference in the two countries social system and cultural attitudes. The two countries can inspire each other and the world in creating better solutions to solve this new form of education inequality.

A unified approach to the Pythagorean identity and projection theorem for a class of divergences based on M-estimations

Divergences that satisfy Pythagorean-type identity are found to be quite useful in statistical inference. Projection theorem of these divergences explores the associated inference problems through closed-form estimators and a fixed number of sufficient statistics. This work attempts to unify the Pythagorean property and projection theorem of such divergences, including the well-known KL, Basu et al., and Jones et al. divergences, minimization of which result in an M-estimation. This unification characterizes a general form of power-law distributions that includes the well-known Student-t and Student-r families. Rao-Blackwell-type best estimators for these families are derived using sufficient statistics based on the proposed unified class of divergences. Finally, it comments on the efficacy of these estimators through numerical studies.

Ancient origin of acetyltransferases catalyzing O-acetylation of plant cell wall polysaccharides.

Members of the domain of unknown function 231 (DUF231)/trichome birefringence-like (TBL) family have been shown to be O-acetyltransferases catalyzing the acetylation of plant cell wall polysaccharides, including pectins, mannan, xyloglucan and xylan. However, little is known about the origin and evolution of plant cell wall polysaccharide acetyltransferases. Here, we investigated the biochemical functions of TBL homologs from Klebsormidium nitens, a representative of an early divergent class of charophyte green algae that are considered to be the closest living relatives of land plants, and Marchantia polymorpha, a liverwort that is an extant representative of an ancient lineage of land plants. The genomes of K. nitens and M. polymorpha harbor two and six TBL homologs, respectively. Biochemical characterization of their recombinant proteins expressed in human embryonic kidney (HEK) 293 cells demonstrated that the two K. nitens TBLs exhibited acetyltransferase activities acetylating the pectin homogalacturonan (HG) and hence were named KnPOAT1 and KnPOAT2. Among the six M. polymorpha TBLs, five of them (MpPOAT1 to 5) possessed acetyltransferase activities toward pectins and the remaining one (MpMOAT1) catalyzed 2-O- and 3-O-acetylation of mannan. While MpPOAT1,2 specifically acetylated HG, MpPOAT3,4,5 could acetylate both HG and rhamnogalacturonan-I (RG-I). Consistent with the acetyltransferase activities of these TBLs, pectins isolated from K. nitens and both pectins and mannan from M. polymorpha were shown to be acetylated. These findings indicate that the TBL genes were recruited as cell wall polysaccharide O-acetyltransferases as early as in charophyte green algae with activities toward pectins and they underwent expansion and functional diversification to acetylate various cell wall polysaccharides during evolution of land plants.

Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.

The extent to which hybridization disrupts a gene's pattern of expression likely governs its propensity for introgression, while its extent of molecular divergence can itself underlie such disruption. Together, these phenomena shape the landscape of sequence and transcriptional divergence across the genome as species diverge. To understand this process, we characterize gene expression inheritance, regulatory divergence, and molecular divergence in the reproductive transcriptomes of species linked by gene flow: the fruit flies Anastrepha fraterculus and A. obliqua, which show evidence of gene flow despite clear evolutionary divergence. We find that their transcriptional patterns are a mosaic between those typically observed within and between allopatric species. Transcripts showing transgressive expression in hybrids or cis-regulatory divergence between species are associated with greater sequence divergence. This may reflect pleiotropic constraints that make them resistant to gene flow or they may be more likely to experience divergent selection. While these more divergent gene classes are likely to be important contributors to species differences, they are relatively rare. Instead, most differentially regulated transcripts, including those linked to reproduction, show high degrees of dominance in hybrids and trans-regulated divergence between species, suggesting widespread genetic compatibility that potentially allowed for introgression. These findings provide insights into how postzygotic isolating mechanisms might evolve in the presence of gene flow: regions showing cis-regulatory divergence or transgressive expression contribute to reproductive isolation, while regions with dominant expression and trans-regulatory divergence allow for introgression. These patterns create a genomic mosaic of transcriptional regulation that is tied to sequence divergence.

Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients

Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.

Characterizing the Functional Density Power Divergence Class

Divergence measures have a long association with statistical inference, machine learning and information theory. The density power divergence and related measures have produced many useful (and popular) statistical procedures, which provide a good balance between model efficiency on one hand and outlier stability or robustness on the other. The logarithmic density power divergence, a particular logarithmic transform of the density power divergence, has also been very successful in producing efficient and stable inference procedures; in addition it has also led to significant demonstrated applications in information theory. The success of the minimum divergence procedures based on the density power divergence and the logarithmic density power divergence (which also go by the names <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\beta $ </tex-math></inline-formula> -divergence and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\gamma $ </tex-math></inline-formula> -divergence, respectively) make it imperative and meaningful to look for other, similar divergences which may be obtained as transforms of the density power divergence in the same spirit. With this motivation we search for such transforms of the density power divergence, referred to herein as the functional density power divergence class. The present article characterizes this functional density power divergence class, and thus identifies the available divergence measures within this construct that may be explored further for possible applications in statistical inference, machine learning and information theory.

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice

ABSTRACT Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel “pathometagenomic” approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

Blow-up solutions for a class of divergence Schrödinger equations with intercritical inhomogeneous nonlinearity

In this article, we study a class of divergence Schrödinger equations with intercritical inhomogeneous nonlinearity i∂tu+∇⋅(|x|b∇u)=−|x|c|u|pu,(x,t)∈Rn×R, where 2 − n &amp;lt; b &amp;lt; 2, c ≥ b − 2, and 2(2 − b) − bp &amp;lt; np − 2c &amp;lt; (2 − b)(p + 2). We prove the blow-up of radial solutions for the negative energy by using a virial-type estimate. In addition, we derive a generalized Gagliardo–Nirenberg inequality and use it to establish the general blow-up criteria for radial solutions with non-negative energy.

A two-step access to fused-/spiro-polycyclic frameworks via double Heck cascade and acid-driven processes.

This report illustrates the rapid construction of two divergent classes of polycyclic frameworks, benzo[a]fluorenones and spiro-chromenone indenes, via a double Heck cascade and an acid-driven cyclization from easily accessible precursors, alkyl 2-bromocinnamate esters and diphenylacetylenes. The present strategy has surveyed a broad substrate scope and delivered an array of products with interesting structural features. Besides, fluorescence studies were performed for the synthesized benzo[a]fluorenones.

Minimum information divergence of Q-functions for dynamic treatment resumes

This paper aims at presenting a new application of information geometry to reinforcement learning focusing on dynamic treatment resumes. In a standard framework of reinforcement learning, a Q-function is defined as the conditional expectation of a reward given a state and an action for a single-stage situation. We introduce an equivalence relation, called the policy equivalence, in the space of all the Q-functions. A class of information divergence is defined in the Q-function space for every stage. The main objective is to propose an estimator of the optimal policy function by a method of minimum information divergence based on a dataset of trajectories. In particular, we discuss the \(\gamma \)-power divergence that is shown to have an advantageous property such that the \(\gamma \)-power divergence between policy-equivalent Q-functions vanishes. This property essentially works to seek the optimal policy, which is discussed in a framework of a semiparametric model for the Q-function. The specific choices of power index \(\gamma \) give interesting relationships of the value function, and the geometric and harmonic means of the Q-function. A numerical experiment demonstrates the performance of the minimum \(\gamma \)-power divergence method in the context of dynamic treatment regimes.

On robustness of model selection criteria based on divergence measures: Generalizations of BHHJ divergence-based method and comparison

In model selection problems, robustness is one important feature for selecting an adequate model from the candidates. We focus on statistical divergence-based selection criteria and investigate their robustness. We mainly consider BHHJ divergence and related classes of divergence measures. BHHJ divergence is a representative robust divergence measure that has been utilized in, for example, parametric estimation, hypothesis testing, and model selection. We measure the robustness against outliers of a selection criterion by approximating the difference of values of the criterion between the population with outliers and the non-contaminated one. We derive and compare the conditions to guarantee robustness for model selection criteria based on BHHJ and related divergence measures. From the results, we find that conditions for robust selection differ depending on the divergence families, and that some expanded classes of divergence measures require stricter conditions for robust model selection. Moreover, we prove that robustness in estimation does not always guarantee robustness in model selection. Through numerical experiments, we confirm the advantages and disadvantages of each divergence family, asymptotic behavior, and the validity for employing criteria on the basis of robust divergence. Especially, we reveal the superiority of BHHJ divergence in robust model selection for extensive cases.

Everyone’s an artist?

This article examines the endurance of traditional class labels among precarious workers in post-recession Dublin. It argues that tensions remain between creatives and non-creatives due to: (1) divergent class concepts, (2) a lack of social engagement, and (3) unequal access to economic, social, and cultural capital, which creatives mobilize to protect some highly vocational artistic labor. It is thus not a shared experience of the same kind of precarious exploitation that unites the precariat but a trap held in common, whereby self-actualization through labor is construed as a route to freedom. Drawing on Karl Marx’s theory of emancipation, I suggest that attempts to redress precarization should focus on undermining this encroachment of work into life, which I argue results in exploitation and alienation for all precarious workers.

Genetic variability for quantitative and quality traits in cowpea [Vigna unguiculata (L.) Walp

The field experiment comprised of&nbsp; 30 cowpea genotypes were evaluated for genetic variability for important quantitative and quality traits during the Summer 2019 season. Analysis of variance showed that there was &nbsp;significant differences among the genotypes evaluated for all the characters studied. A &nbsp;high value of phenotypic coefficient of variation than genotypic coefficient of variation was &nbsp;observed for all the characters which revealed the influence of environment for phenotypic expression of the traits. High heritability and the high genetic advance were &nbsp;observed for days to 50% flowering, leaf width, the number of nodes on main stem, the number of main branches, the number of pods per plant, length of pod, the number of seeds per pod, test weight, seed yield per plant, fat content, lignin content and host preference mechanism of pulse beetle on the grain of cowpea indicating that the characters are governed by additive gene action and the characters which can be improved by simple selection. On Mahalanobis D2 statistics, the genotypes were grouped into four clusters. A &nbsp;maximum number of genotypes was observed in &nbsp;cluster I with 16 genotypes followed by clusters II and III with 8 genotypes each and cluster IV with solitary genotype. On the basis of divergence classes studied the genotypes viz., PMCP-1021, CP-20, CP-25, CP-26, CP-7, CP-2-1, CP-15, CP-9-1, CP-17, CP-2-1, PCP-1809, PCP-1124, PCP-1123, Phule Rukmini and Phule Pandhari can be used for the further breeding programme. &nbsp; Keywords: Cowpea, Genetic diversity, Heritability, Genetic advance

Identification of a broad lipid repertoire associated to the endothelial cell protein C receptor (EPCR)

Evidence is mounting that the nature of the lipid bound to the endothelial cell protein C receptor (EPCR) has an impact on its biological roles, as observed in anticoagulation and more recently, in autoimmune disease. Phosphatidylethanolamine and phosphatidylcholine species dominate the EPCR lipid cargo, yet, the extent of diversity in the EPCR-associated lipid repertoire is still unknown and remains to be uncovered. We undertook mass spectrometry analyses to decipher the EPCR lipidome, and identified species not yet described as EPCR ligands, such as phosphatidylinositols and phosphatidylserines. Remarkably, we found further, more structurally divergent lipids classes, represented by ceramides and sphingomyelins, both in less abundant quantities. In support of our mass spectrometry results and previous studies, high-resolution crystal structures of EPCR in three different space groups point to a prevalent diacyl phospholipid moiety in EPCR’s pocket but a mobile and ambiguous lipid polar head group. In sum, these studies indicate that EPCR can associate with varied lipid classes, which might impact its properties in anticoagulation and the onset of autoimmune disease.

Differential Responses to Yellow-Rust Stress Assist in the Identification of Candidate Wheat (Triticum aestivum L.) Genotypes for Resistance Breeding

Yellow rust (YR) globally affects wheat crops. It may turn into an epidemic, resulting in significant yield losses if the environment is suited to YR spread. The provision of resistant wheat cultivars is a sustainable protection strategy against YR. The current study aimed to use a combination of classical analytical tools to identify potential wheat lines through screening under YR stress for utilization in YR-resistance breeding. A total of 14 parents, which included 9 lines and 5 testers, were formed into 45 cross combinations via line × tester mating format. The tested germplasm was grown in a triplicate randomized full-block design, under optimal and yellow rust (YR)-stress conditions. Data were recorded on different morphological, physiochemical, yield and component traits at appropriate crop stages. A pre-combining ability analysis revealed significant inter-genotype variations. A combining ability study identified non-additive gene action in the inheritance of most of the investigated traits. Four potential parents (PR128, AN179, KS17 and WD17) and two crosses (PR128 × WD17 and AN179 × KS17) retained higher combining ability values for yield traits under YR-stress. A cluster analysis based on the overall performance found divergent classes among the screened genotypes. The clustering of different genotypes was shifted under YR-stress, which suggests variable genotypic response. Through factor analysis, we assessed and confirmed genotypes performing consistently under YR-stress. The identified genotypes may be used for disease-resistance breeding in wheat. Based on their positive correlation with grain yield, we suggest the use of peduncle length and tillers per plant as phenotypic markers for wheat selection and breeding. The knowledge base generated through the current study will add to the ongoing research on sustainable wheat breeding program.

Lac-extract doped polyaniline nano-ribbons as fluorescence sensor and molecular switch for detection of aqueous AsO43− and Fe3+ contaminants

Detection of contaminants dissolved in water is an essential step for water quality monitoring and can guide us from consuming unhealthy water. Herein, we demonstrate the development of a novel low-cost polymer by doping polyaniline nanoribbons with lac-extract (LAC-PANI) and report its excellent fluorescence sensing properties against aqueous AsO43− and Fe3+ ions, both of which AsO43− and Fe3+can pose health hazard for humans with the former being extremely toxic. When excited with radiation of 320 nm, the sensor showed contrasting fluorescence response against AsO43− and Fe3+ ions as the luminescence intensity showed sharp quenching upon exposure to Fe3+ but against AsO43− it showed a sharp rise in intensity. When other cations and oxoanions were concurrently tested with Fe3+ and AsO43− respectively, the sensor showed high specificity only to these two ions. Furthermore, a reversible and distinct fluorescence turn on–off-on switching response was observed upon sequential addition of AsO43−, Fe3+ and AsO43− ions which points to the utility of the sensor as a NOT-AND compound molecular logic gate for simultaneous detection of two electronically divergent analyte classes. Thus, the LAC-PANI sensor developed in this work shows enormous potential for next generation fluorescence sensor useful for water quality monitoring.

Quantum metrics based upon classical Jensen–Shannon divergence

Jensen–Shannon divergence is an important distinguishability measure between probability distributions that finds interesting applications within the context of Information Theory. In particular, this classical divergence belongs to a remarkable class of divergences known as Csiszár or f-divergences. In this paper we analyze the problem of obtaining a distance measure between two quantum states starting from the classical Jensen–Shannon divergence between two probability distributions. Considering the Jensen–Shannon divergence as a Csiszár divergence, we first focus on the problem of distinguishability between two pure quantum states. We find a quantum version of the classical Jensen–Shannon divergence that differs from the previously introduced Quantum Jensen–Shannon Divergence. The two quantum versions of Jensen–Shannon divergence have different interpretations within the framework of Quantum Information Theory. Whereas the former quantum version of Jensen–Shannon divergence can be interpreted as the Holevo bound, the alternative quantum version obtained in this work equals the accessible information. Furthermore, we obtain a monoparametric family of metrics between two quantum pure states. Finally, we extend this family of metrics to the case of mixed quantum states by means of the concept of purification.

Serotonergic Paracrine Targets in the Intestinal Mucosa.

Serotonin functions as a neurotransmitter in the enteric nervous system. Aside from its neurotransmitter role, serotonin also is a paracrine mediatorial signal in the digestive tract. It is a major paracrine signaling molecule in the integrated physiology of several classes of cells in the intestinal mucosa. Paracrine action can be initiation or suppression of activity in populations of cells that make up divergent phenotypic classes. This underlies phenotypic plasticity in single classes and links single classes to other neighboring phenotypic classes, thereby forming a single and higher-order organization in which different categories of function are integrated to work in harmony as a single homeostatic entity at higher levels of physiological organization. Phenotypic classes of cells that are linked by serotonergic paracrine signaling at upper levels of functional organization in the small intestine are (1) enterochromaffin cells; (2) enteric mast cells; (3) spinal sensory afferents; (4) sympathetic postganglionic neurons; (5) enteric neurons.