Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits.

Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. Theoretically, selection across different spatial scales, i.e. between- and within-hosts, shapes these trade-offs. However, trade-offs are also dependent on parasite biology. Despite their applied importance the evolution of virulence in fungal parasites is poorly understood: virulence can be unstable in culture and commonly fails to increase in simple passage experiments. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for speed of kill, parasite yield or infectivity by manipulating competition within and between hosts and between-populations of hosts over 7 rounds of infection. We characterized ancestral and evolved lineages by whole genome sequencing and by measuring virulence, growth rate, sporulation and fitness. While several lineages showed increases in virulence, we saw none of the trade-offs commonly found in obligately-killing parasites. Phenotypically similar lineages within treatments often shared multiple single-nucleotide variants, indicating strong convergent evolution. The most dramatic phenotypic changes were in timing of sporulation and spore production in vitro. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits-virulence and spore production-that are often in conflict in other parasites.

Characterization of chromosomal segment substitution lines developed in the genetic background of rice variety K 343.

In this study, BC3F2 convergent population [(K343*3/RML22 × K343*3/DHMAS) × K343] was constructed by marker-assisted backcross breeding using K343 as the recurrent parent. DHMAS and RML22 were used as donor parents for the rice blast resistance genes Pi54 and Pi9, respectively. The population was first characterized using GGT 2.0 software, which showed 96.7% of the recurrent genome recovery covering 13953.6 cM, while DHMAS and RML22 showed 1.6% (235.5 cM) and 1.2% (177.1 cM) introgression respectively. The chromosomal segment substitution lines (CSSLs) were then identified using CSSL Finder software. A total of 36 CSSLs were identified, including 22 for DHMAS/K343 and 14 for RML22/K343. Introgression rates for donor substituted segments in DHMAS/K343 CSSLs ranged from 0.54% to 5.99%, with donor coverage of 44.5%, while in RML22/K343 CSSLs, introgression rates ranged from 0.54% to 4.75%, with donor coverage of 24.5%. The identified CSSLs would be a valuable genetic pool and could be used as genomic resources for the discovery and mapping of important genes and QTLs in rice genetic improvement.

A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 2: Non-DSM compounds.

Malaria remains a severe global health concern, with 249 million cases reported in 2022, according to the World Health Organization (WHO) [1]. PfDHODH is an essential enzyme in malaria parasites that helps to synthesize certain building blocks for their growth and development. It has been confirmed that targeting Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme could lead to new and effective antimalarial drugs. Inhibitors of PfDHODH have shown potential for slowing down parasite growth during both the blood and liver stages. Over the last two decades, many species selective PfDHODH inhibitors have been designed, including DSM compounds and other non-DSM compounds. In the first chapter [2] of this review, we have reviewed all synthetic schemes and structure-activity relationship (SAR) studies of DSM compounds. In this second chapter, we have compiled all the other non-DSM PfDHODH inhibitors based on dihydrothiophenones, thiazoles, hydroxyazoles, and N-alkyl-thiophene-2-carboxamides. The review not only offers an insightful overview of the synthetic methods employed but also explores into alternative routes and innovative strategies involving different catalysts and chemical reagents. A critical aspect covered in the review is the SAR studies, which provide a comprehensive understanding of how structural modifications impact the efficacy of PfDHODH inhibitors and challenges related to the discovery of PfDHODH inhibitors. This information is invaluable for scientists engaged in the development of new antimalarial drugs, offering insights into the most promising scaffolds and their synthetic techniques.

A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 1: triazolopyrimidine, isoxazolopyrimidine and pyrrole-based (DSM) compounds.

One of the deadliest infectious diseases, malaria, still has a significant impact on global morbidity and mortality. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in de novo pyrimidine nucleotide biosynthesis and has been clinically validated as an innovative and promising target for the development of novel targeted antimalarial drugs. PfDHODH inhibitors have the potential to significantly slow down parasite growth at the blood and liver stages. Several PfDHODH inhibitors based on various scaffolds have been explored over the past two decades. Among them, triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based derivatives known as DSM compounds showed tremendous potential as novel antimalarial agents, and one of the triazolopyrimidine-based compounds (DSM265) was able to reach phase IIa clinical trials. DSM compounds were synthesized as PfDHODH inhibitors with various substitutions based on structure-guided medicinal chemistry approaches and further optimised as well. For the first time, this review provides an overview of all the synthetic approaches used for the synthesis, alternative synthetic routes, and novel strategies involving various catalysts and chemical reagents that have been used to synthesize DSM compounds. We have also summarized SAR study of all these PfDHODH inhibitors. In an attempt to assist readers, scientists, and researchers involved in the development of new PfDHODH inhibitors as antimalarials, this review provides accessibility of all synthetic techniques and SAR studies of the most promising triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based PfDHODH inhibitors.

Automated detection of Bornean white-bearded gibbon (Hylobates albibarbis) vocalizations using an open-source framework for deep learning.

Passive acoustic monitoring is a promising tool for monitoring at-risk populations of vocal species, yet, extracting relevant information from large acoustic datasets can be time-consuming, creating a bottleneck at the point of analysis. To address this, an open-source framework for deep learning in bioacoustics to automatically detect Bornean white-bearded gibbon (Hylobates albibarbis) "great call" vocalizations in a long-term acoustic dataset from a rainforest location in Borneo is adapted. The steps involved in developing this solution are described, including collecting audio recordings, developing training and testing datasets, training neural network models, and evaluating model performance. The best model performed at a satisfactory level (F score = 0.87), identifying 98% of the highest-quality calls from 90 h of manually annotated audio recordings and greatly reduced analysis times when compared to a human observer. No significant difference was found in the temporal distribution of great call detections between the manual annotations and the model's output. Future work should seek to apply this model to long-term acoustic datasets to understand spatiotemporal variations in H. albibarbis' calling activity. Overall, a roadmap is presented for applying deep learning to identify the vocalizations of species of interest, which can be adapted for monitoring other endangered vocalizing species.

Transcriptomic responses of females to consumption of nuptial food gifts as a potential mediator of sexual conflict in decorated crickets.

Nuptial food gift provisioning by males to females at mating is a strategy in many insects that is thought to be shaped by sexual conflict or sexual selection, as it affords males access to a female's physiology. While males often attempt to use these gifts to influence female behaviour to their own advantage, females can evolve counter mechanisms. In decorated crickets, the male's nuptial gift comprises part of the spermatophore, the spermatophylax, the feeding on which deters the female from prematurely terminating sperm transfer. However, ingested compounds in the spermatophylax and attachment of the sperm-containing ampulla could further influence female physiology and behaviour. We investigated how mating per se and these two distinct routes of potential male-mediated manipulation influence the female transcriptomic response. We conducted an RNA sequencing experiment on gut and head tissues from females for whom nuptial food gift consumption and receipt of an ejaculation were independently manipulated. In the gut tissue, we found that females not permitted to feed during mating exhibited decreased overall gene expression, possibly caused by a reduced gut function, but this was countered by feeding on the spermatophylax or a sham gift. In the head tissue, we found only low numbers of differentially expressed genes, but a gene co-expression network analysis revealed that ampulla attachment and spermatophylax consumption independently induce distinct gene expression patterns. This study provides evidence that spermatophylax feeding alters the female post-mating transcriptomic response in decorated crickets, highlighting its potential to mediate sexual conflict in this system.

Correction: Pd-Catalysed [3 + 2]-cycloaddition towards the generation of bioactive bis-heterocycles/identification of COX-2 inhibitors via in silico analysis.

Correction for 'Pd-Catalysed [3 + 2]-cycloaddition towards the generation of bioactive bis-heterocycles/identification of COX-2 inhibitors via in silico analysis' by Elagandhula Sathish et al., Org. Biomol. Chem., 2022, 20, 4746-4752, https://doi.org/10.1039/D2OB00467D.

Diversity-oriented synthesis yields novel multistage antimalarial inhibitors.

Antimalarial drugs have thus far been chiefly derived from two sources-natural products and synthetic drug-like compounds. Here we investigate whether antimalarial agents with novel mechanisms of action could be discovered using a diverse collection of synthetic compounds that have three-dimensional features reminiscent of natural products and are underrepresented in typical screening collections. We report the identification of such compounds with both previously reported and undescribed mechanisms of action, including a series of bicyclic azetidines that inhibit a new antimalarial target, phenylalanyl-tRNA synthetase. These molecules are curative in mice at a single, low dose and show activity against all parasite life stages in multiple in vivo efficacy models. Our findings identify bicyclic azetidines with the potential to both cure and prevent transmission of the disease as well as protect at-risk populations with a single oral dose, highlighting the strength of diversity-oriented synthesis in revealing promising therapeutic targets.

Changes in temperature alter the potential outcomes of virus host shifts.

Host shifts-where a pathogen jumps between different host species-are an important source of emerging infectious disease. With on-going climate change there is an increasing need to understand the effect changes in temperature may have on emerging infectious disease. We investigated whether species' susceptibilities change with temperature and ask if susceptibility is greatest at different temperatures in different species. We infected 45 species of Drosophilidae with an RNA virus and measured how viral load changes with temperature. We found the host phylogeny explained a large proportion of the variation in viral load at each temperature, with strong phylogenetic correlations between viral loads across temperature. The variance in viral load increased with temperature, while the mean viral load did not. This suggests that as temperature increases the most susceptible species become more susceptible, and the least susceptible less so. We found no significant relationship between a species' susceptibility across temperatures, and proxies for thermal optima (critical thermal maximum and minimum or basal metabolic rate). These results suggest that whilst the rank order of species susceptibilities may remain the same with changes in temperature, some species may become more susceptible to a novel pathogen, and others less so.

Structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase-dihydropteroate synthase from Plasmodium vivax sheds light on drug resistance.

The genomes of the malaria-causing Plasmodium parasites encode a protein fused of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) domains that catalyze sequential reactions in the folate biosynthetic pathway. Whereas higher organisms derive folate from their diet and lack the enzymes for its synthesis, most eubacteria and a number of lower eukaryotes including malaria parasites synthesize tetrahydrofolate via DHPS. Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) HPPK-DHPSs are currently targets of drugs like sulfadoxine (SDX). The SDX effectiveness as an antimalarial drug is increasingly diminished by the rise and spread of drug-resistant mutations. Here, we present the crystal structure of PvHPPK-DHPS in complex with four substrates/analogs, revealing the bifunctional PvHPPK-DHPS architecture in an unprecedented state of enzymatic activation. SDX's effect on HPPK-DHPS is due to 4-amino benzoic acid (pABA) mimicry, and the PvHPPK-DHPS structure sheds light on the SDX-binding cavity, as well as on mutations that effect SDX potency. We mapped five dominant drug resistance mutations in PvHPPK-DHPS: S382A, A383G, K512E/D, A553G, and V585A, most of which occur individually or in clusters proximal to the pABA-binding site. We found that these resistance mutations subtly alter the intricate enzyme/pABA/SDX interactions such that DHPS affinity for pABA is diminished only moderately, but its affinity for SDX is changed substantially. In conclusion, the PvHPPK-DHPS structure rationalizes and unravels the structural bases for SDX resistance mutations and highlights architectural features in HPPK-DHPSs from malaria parasites that can form the basis for developing next-generation anti-folate agents to combat malaria parasites.

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read-filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in nonlaboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception among others. A large proportion of potential noncoding RNA transcripts present in our differentially expressed set provide first evidence of a possible role for long noncoding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from positive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.

Sexual conflict over mating in Gnatocerus cornutus? Females prefer lovers not fighters.

Female mate choice and male-male competition are the typical mechanisms of sexual selection. However, these two mechanisms do not always favour the same males. Furthermore, it has recently become clear that female choice can sometimes benefit males that reduce female fitness. So whether male-male competition and female choice favour the same or different males, and whether or not females benefit from mate choice, remain open questions. In the horned beetle, Gnatocerus cornutus, males have enlarged mandibles used to fight rivals, and larger mandibles provide a mating advantage when there is direct male-male competition for mates. However, it is not clear whether females prefer these highly competitive males. Here, we show that female choice targets male courtship rather than mandible size, and these two characters are not phenotypically or genetically correlated. Mating with attractive, highly courting males provided indirect benefits to females but only via the heritability of male attractiveness. However, mating with attractive males avoids the indirect costs to daughters that are generated by mating with competitive males. Our results suggest that male-male competition may constrain female mate choice, possibly reducing female fitness and generating sexual conflict over mating.

Enhancing gait recognition by multimodal fusion of mobilenetv1 and xception features via PCA for OaA-SVM classification.

Gait recognition has become an increasingly promising area of research in the search for noninvasive and effective methods of person identification. Its potential applications in security systems and medical diagnosis make it an exciting field with wide-ranging implications. However, precisely recognizing and assessing gait patterns is difficult, particularly in changing situations or from multiple perspectives. In this study, we utilized the widely used CASIA-B dataset to observe the performance of our proposed gait recognition model, with the aim of addressing some of the existing limitations in this field. Fifty individuals are randomly selected from the dataset, and the resulting data are split evenly for training and testing purposes. We begin by excerpting features from gait photos using two well-known deep learning networks, MobileNetV1 and Xception. We then combined these features and reduced their dimensionality via principal component analysis (PCA) to improve the model's performance. We subsequently assessed the model using two distinct classifiers: a random forest and a one against all support vector machine (OaA-SVM). The findings indicate that the OaA-SVM classifier manifests superior performance compared to the others, with a mean accuracy of 98.77% over eleven different viewing angles. This study is conducive to the development of effective gait recognition algorithms that can be applied to heighten people's security and promote their well-being.

The condition-dependence of male genital size and shape.

The male genitals of internal fertilisers evolve rapidly and divergently, and sexual selection is generally responsible for this. Many sexually selected traits are condition-dependent-with their expression dependent upon the resources available to be allocated to them-as revealed by genetic or environmental manipulations of condition. However, it is not clear whether male genitals are also condition-dependent. Here we manipulate condition in two ways (via inbreeding and diet) to test the condition-dependence of the genital arch of Drosophila simulans. We found that genital size but not genital shape suffered from inbreeding depression, whereas genital size and shape were affected by dietary manipulation of condition. The differential effects of these treatments likely reflect underlying genetic architecture that has been shaped by past selection: inbreeding depression is only expected when traits have a history of directional selection, while diet impacts traits regardless of historical selection. Nonetheless, our results suggest genitals can be condition-dependent like other sexually selected traits.

Structure-guided discovery of adenosine triphosphate-competitive casein kinase 2 inhibitors.

Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic serine-threonine kinase. CK2 has been identified as a potential drug target for the treatment of cancer and related disorders. Several adenosine triphosphate-competitive CK2 inhibitors have been identified and have progressed at different levels of clinical trials. This review presents details of CK2 protein, structural insights into adenosine triphosphate binding pocket, current clinical trial candidates and their analogues. Further, it includes the emerging structure-based drug design approaches, chemistry, structure-activity relationship and biological screening of potent and selective CK2 inhibitors. The authors tabulated the details of CK2 co-crystal structures because these co-crystal structures facilitated the structure-guided discovery of CK2 inhibitors. The narrow hinge pocket compared with related kinases provides useful insights into the discovery of CK2 inhibitors.

Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents.

Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.

Dataset for classifying English words into difficulty levels by undergraduate and postgraduate students.

The ability of a student to know the meaning of a word depends on the level of education they are at. Since most information is stored in text, students use electronic gadgets to obtain information about their study subjects. This Dataset provides the classification of English words into difficulty levels as viewed by the students at graduation and post-graduation levels. The Dataset in the consideration categorizes the English words into difficulty levels as viewed by undergraduate and postgraduate students in non-native English-speaking countries like India. Some words are neither considered difficult by undergraduate nor postgraduate students. The Dataset can help researchers provide meaning to difficult English words in native languages at runtime (while reading a text document). The Dataset can also help authors write their books and articles for undergraduate and postgraduate levels in different tones, keeping their vocabulary in view.

De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests.

The entomopathogenic fungus Akanthomyces muscarius is commonly used in agriculture to manage insect pests. Besides its use as a commercially important biological control agent, it also presents a potential model for studying host-pathogen interactions and the evolution of virulence in a laboratory setting. Here, we describe the first high-quality genome sequence for A. muscarius. We used long- and short-read sequencing to assemble a sequence of 36.1 Mb with an N50 of 4.9 Mb. Genome annotation predicted 12347 genes, with 96.6 % completeness based on the core Hypocrealen gene set. The high-quality assembly and annotation of A. muscarius presented in this study provides an essential tool for future research on this commercially important species.

Wilderness areas under threat from global redistribution of agriculture.

Agriculture expansion is already the primary cause of terrestrial biodiversity loss globally1,2; yet, to meet the demands of growing human populations, production is expected to have to double by 2050.3 The challenge of achieving expansion without further detriment to the environment and biodiversity is huge and potentially compounded by climate change, which may necessitate shifting agriculture zones poleward to regions with more suitable climates,4 threatening species or areas of conservation priority.5,6,7 However, the possible future overlap between agricultural suitability and wilderness areas, increasingly recognized for significant biodiversity, cultural, and climate regulation values, has not yet been examined. Here, using high-resolution climate data, we model global present and future climate suitability for 1,708 crop varieties. We project, over the next 40 years, that 2.7 million km2 of land within wilderness will become newly suitable for agriculture, equivalent to 7% of the total wilderness area outside Antarctica. The increase in potentially cultivable land in wilderness areas is particularly acute at higher latitudes in the northern hemisphere, where 76.3% of newly suitable land is currently wilderness, equivalent to 10.2% of the total wilderness area. Our results highlight an important and previously unidentified possible consequence of the disproportionate warming known to be occurring in high northern latitudes. Because we find that, globally, 72.0% of currently cultivable land is predicted to experience a net loss in total crop diversity, agricultural expansion is a major emerging threat to wilderness. Without protection, the vital integrity of these valuable areas could be irreversibly lost.

Clinical and Biochemical Correlation of Intra-articular Platelet-Rich Plasma and Corticosteroid Using Serum Matrix Metalloproteinase 3 (MMP-3) Levels in Osteoarthritis of Knee.

Introduction Osteoarthritis (OA) in humans is an inevitable consequence of ageing and can now be effectively managed with advancements in knowledge and understanding of the disease. The major concern in a patient suffering from this disease is the functional impairment caused by the pain. The goals in the management of OA knee include symptom relief with preservation of joint function. Despite there being a number of studies on the effectiveness of PRP and CS for knee OA, most of them have focused on patient-reported functional outcomes only. Hence, we conducted this study to assess the potential and effectiveness of a single intra-articular injection of PRP and CS in the functional improvement of knee OA patients using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Visual Analogue Scale (VAS) and to establish the bio-modulatory effects of intra-articular PRP and CS in knee OA patients by estimating the serum matrix metalloproteinase-3 (MMP-3) levels. Methodology Patients attending the outpatient department with complaints of knee pain were screened. Standing anteroposterior and lateral radiographs of the knees were obtained. Patients with Kellgren and Lawrence (K-L) grades II and III were enrolled in our study. A total of 96 patients were included in the study after fulfilling the inclusion and exclusion criteria. Patients were divided into two groups (PRP and CS) by randomisation. There were 48 each in the PRP and CS groups, out of which nine were lost to follow-up, two from the PRP group and seven from the CS group. A total of 87 patients fulfilling the inclusion criteria were finally enrolled in the study and followed up for nine months after a single intra-articular injection. The biochemical assessment of serum levels of MMP-3 was done at baseline and in the ninth month. Accordingly, patients in the PRP group were injected with freshly prepared PRP (3 ml) within two hours of preparation, whereas those in the CS received 80 mg of methylprednisolone acetate. VAS and WOMAC were measured at baseline, and then in the first, third, sixth, and ninth month post-injection follow-ups. MMP-3 level was estimated before the injection and at the ninth-month post-injection follow-up. Data collected for both groups were analysed and compared with each other. Conclusion PRP is unquestionably a better option than CS in OA of the knee based on boosting functional activity, lowering stiffness, and reducing pain, all three of which are denoted by the WOMAC and VAS scores as the effect of PRP lasts longer than CS injections for the aforesaid issues. We could not find any significant change in levels of MMP3 post PRP and CS injections, which signifies that these two modalities do not have any effect in either preventing cartilage degeneration or promoting cartilage regeneration. Our findings have shown that PRP injections are safe, minimally invasive, and effective treatment modalities for OA knee.