Explore the vast range of titles available.

The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

BackgroundThe tumor microenvironment (TME) of GBM consists of not only tumor cells, but stromal cells, oligodendrocytes, and myeloid cells. Due to its highly invasiveness and frequent mutations, treatment options are limited. GBM tumors often exhibit dysregulation of tyrosine kinases, such as EGFR, VEGFR, and PDGFRa, making tyrosine kinase inhibitors (TKIs) a potential treatment option. Although preclinical studies have yielded positive outcomes in slowing tumor growth, the overall impact on patient survival is limited. Hereafter, this study uses Bayesian inference to understand the aberrant kinase activities in tumor tissues.MethodsWe established a co-culture of U87 cells and THP1-induced macrophages. Co-cultures were then digested and phosphopeptides were then enriched for pTyr. We used KSTAR1 to compute the kinase activities of both co-culture and GBM tissues from CPTAC-3 project.2 We first established thresholds for individual batches and identify the phosphosites to be included in the calculation. We then visualized the activities using ‘DotPlot’ function. We used Cibersort3 to deconvolve GBM tissues. We borrowed a previously published signature matrix.4 We used S-model for batch correction, disabled quantile normalization, and used ran 100 permutations. In the Bayesian model, the prior represents the distributions of the parameters: EGFR amplification (EGFRamp) status, the proportions of tumor and myeloid cells, and a global shrinkage prior. The model was built using pymc package.ResultsIn-vitro cultures of macrophages and U87 show heterogeneous kinase profiles. EGFR, ERBB2, and PDGFRB increased with the proportions of U87, while BTK, CSF1R, and LCK increased with the proportion of macrophages (figure 1). In most tumor tissues, there were 10-30% of myeloid cells and 60-80% tumor cells (including stem cells). Bayesian results (figure 2) showed in tumor tissues, there were a lot more nuances compared to co-cultures. While tumor cells and macrophages in tissues can exhibit various phenotypes, some of the observations from co-cultures still held true. The infiltration of myeloid cells increased CSF1R and did not change EGFR activities, suggesting EGFR mostly relied on the presence of tumor cells. This also suggested myeloid cells were donating CSF1R-relevant substrates and promoting CSF1R activity. EGFR, ERBB2/3/4, and TYK2 were higher in EGFRamp tissues, suggesting EGFRamp may depend on these kinases for signaling.ConclusionsHere, we presented a Bayesian framework to identify the influences of EGFRamp status and cell type proportions in kinase activity prediction While results merited further experimental validation, this facilitated our understanding on tumor heterogeneity in terms of kinase signaling.AcknowledgementsResearch reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA284193. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Interdisciplinary Training in Systems & Biomolecular Data Science Statement: ‘Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number T32GM145443. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Croucher Foundation.ReferencesCrowl S, Jordan BT, Ahmed H, et al. KSTAR: an algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nat Commun. 2022;13:4283. https://doi.org/10.1038/s41467-022-32017-5Multi-scale signaling and tumor evolution in high-grade gliomas. Liu, Jingxian, Agarwal, Anupriya, et al. Cancer Cell. 42:7:1217–1238.e19Newman AM, Steen CB, Liu CL, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37:773–782. https://doi.org/10.1038/s41587-019-0114-2Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D’Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW; GLASS Consortium. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell. 2022 Jun 9;185(12):2184-2199.e16. doi: 10.1016/j.cell.2022.04.038. Epub 2022 May 31. PMID: 35649412; PMCID: PMC9189056.Abstract 1104 Figure 1Kinase activity prediction in U87 and macrophage co-cultures[Image Omitted. See PDF.]Abstract 1104 Figure 2Bayesian model shows the effects of EGFR amplification status, myeloid proportion, and tumor cell proportions[Image Omitted. See PDF.]

The evolutionary potential of a population is shaped by the genetic architecture of its life-history traits. Early-life phenotypes are influenced by both maternal and offspring genotype, and efforts to understand life-history evolution therefore require consideration of the interactions between these separate but correlated genomes. We used a four-generation experimental pedigree to estimate the genetic architecture of early-life phenotypes in a species with dramatic variation in larval size and morphology. In the polychaete annelid Streblospio benedicti, females make either many small eggs that develop into complex larvae that feed in the plankton or few large eggs that develop into benthic juveniles without having to feed as larvae. By isolating the contributions of maternal, paternal, and zygotic genotype to larval traits, we determined that larval anatomical structures are governed by the offspring genotype at a small number of large-effect loci. Larval size is not shaped by the larva’s own genotype but instead depends on loci that act in the mother, and at two genomic locations, by loci that act in the father. The overall phenotype of each larva thus depends on three separate genomes, and a population’s response to selection on larval traits will reflect the interactions among them.

Plant-pollinator mutualisms play a central role in the ecology and evolution of terrestrial ecosystems. Nonetheless, and despite a long history of study, major knowledge gaps persist. There is still much to learn regarding how plant-pollinator relationships are responding to a changing world, and how they function in understudied systems, particularly in the tropics and in the forest canopy. This dissertation draws on two long-term monitoring datasets that were generously shared with me—one from New Jersey and one from Indonesian Borneo— as well as original fieldwork I conducted in the canopy of a tropical peat swamp forest, to explore questions relating to temporal trends in the abundances of pollinators, the flowering phenology of tropical trees, and the structure of interactions between plants and pollinators in the forest canopy.Between 2005 and 2012, the Winfree lab group conducted multiple studies on bee visitation and pollination in watermelon fields in New Jersey and Pennsylvania. Soon after joining the lab in 2020, it occurred to me to use the data from those studies to conduct a longitudinal analysis of trends in bee abundance. Little is known about the population dynamics of bees, especially in the context of agricultural environments where they provide critical pollination services to crop plants. In Chapter 1, we show that bee abundances declined sharply over the 8-year period but also fluctuated wildly from year to year. To differentiate trends from noise, we applied a permutational model that allowed for stochastic variation in bee populations between years. Results of the permutational tests were non-significant, highlighting the importance of accounting for typical annual fluctuations in pollinator abundance when describing long-term trends, as well as the need for more long-term monitoring of pollinator communities.In 2021, I decided that I wanted to conduct research on pollination and pollinators at the Tuanan Research Center, a Rutgers affiliated facility in Central Kalimantan, Indonesia. Unfortunately, Indonesia’s borders were shut to foreign researchers due to the COVID-19 pandemic. Consequently, I turned to existing long-term phenology monitoring data from Tuanan for Chapter 2, which investigates patterns of asynchronous flowering and their implications in tropical rainforest trees. Asynchronous flowering can result in temporal mate restriction, which under certain conditions can lower effective population sizes, reduce genetic diversity, and lead to inbreeding. Tropical peat swamp trees may be among the most asynchronously flowering plant communities known, yet studies of intra-population variation in phenology are lacking for these tree species. Using 18 years of phenology data for 24 tree species, we found that the same conspecific trees tend to flower together across flowering events, but did not find patterns that would lead to lifetime restriction of parental pairings. Taken together with a lack of spatial autocorrelation in phenology, these results do not suggest that temporal mate restriction is likely to have a substantial impact on the genetic structure and genetic health of these tree populations.In 2022 Indonesia opened its borders to foreign researchers, and I was finally able to collect my own data in the field. I travelled to Tuanan on a Fulbright scholarship, where I spent 10 months observing floral interactions in the canopies of 15 species of trees and shrubs in the genus Syzygium. Syzygium is one of the most diverse tree genera in the world, and one of the least understood. In Chapter 3, we provide the first thorough description of pollination mutualisms in Bornean Syzygium and identify relationships between visitor attraction and floral traits in the genus. Communities of Syzygium visitors at Tuanan were similar to those described elsewhere, but we also encountered some unexpected differences, including a few predominantly beetle-visited species, a lack of honeybees, and low rates of nocturnal visitation.A feature of the floral morphology of Syzygium is that it is easy to determine whether visitors are foraging on nectar, pollen, or both during their visits. In Chapter 4, we take advantage of this to build parallel networks of visitation, pollen-use, and nectar-use, and then compare estimates of foraging specialization across the three networks. We found that the community of animals visiting Syzygium flowers was more specialized in their use of nectar as a resource than pollen, contrary to general expectations for specialization in anthophilous animals. Furthermore, the visitation network did not accurately represent resource specialization by flower visiting taxa, an important consideration given the widespread use of visitation-based plant-pollinator networks in current research on pollination mutualisms.These chapters represent a broad range of systems, questions, and methodologies. Yet each one addresses a currently relevant topic in anthecology where substantial knowledge gaps persist, where analytical methods are frequently misapplied, or both.

A social insect colony is a self-organized system with a few reproductive queens and multiple sterile workers performing various tasks cooperatively. As a result, the colony as a whole is a unit of selection. Most social insects are clustered within the order Hymenoptera. Haplodiploidy within this order (and beyond) leads to unusual relatedness among sisters, and this has been hypothesized to promote the evolution of cooperation. Workers can use different communication systems to coordinate recruitment to food sources and to perform various other tasks. Social insect colonies can face various problems, such as environmental perturbations, internal errors, and competition from other colonies. My thesis aims to understand how social insects respond to these problems and to understand whether haplodiploidy drives the evolution of eusociality. Specifically, my thesis accomplishes the following:(1) I applied a robustness mechanism categorization framework from systems biology to understand how individual Solenopsis xyloni workers respond to a perturbation of an already established pheromone trail using a classic T-maze setup. I found that S. xyloni workers abandoned the sucrose feeder when the already established pheromone trail was perturbed. Ants that managed to make a choice with the disrupted trail made random choices and did not reinforce the pheromone trail. However, when the sucrose concentration in the feeder was doubled, ants were less likely to abandon the trail, but continued to make random choices, and did not reinforce the pheromone trail. This study suggests a way forward to systematically study individual and collective responses to different perturbations.(2) I designed an agent-based model in Netlogo to examine how different types of errors affect collective foraging outcomes, and how different communication systems modify these outcomes. Overall, I found that errors led to decreased exploration and exploitation. Errors that had a high probability of occurring (false positive and forgetting errors) were the most detrimental to collective foraging performance. Communication overall improved resource collection rate and efficiency, but surprisingly led to an increased exploration for resources. In addition, communication presence mitigated the effects of errors rather than exacerbating them (i.e., there were no misinformation cascades). The results from my model suggest that the evolution of communication systems may also have been shaped by selection on exploration and robustness against different error types, as well as selection on efficient foraging.(3) I examined whether individual Temnothorax rugatulus ants can assess each other’s fighting abilities during a dyadic contest. I used contest duration as the response variable, and dry weight (proxy for body size) and head width (proxy for weaponry) as proxies of fighting abilities. I found that neither proxy of fighting abilities predicted the contest duration, indicating an absence of assessment. However, since I did not provide any resource for the ants to fight over, the ants may not have perceived this interaction as a contest. My study shows that individual contests are not identical to colony-level contests, and needs further investigation.(4) I investigated whether the evolution of eusociality is correlated with the evolution of haplodiploidy using a family-level hexapod phylogeny. I used three phylogenetic comparative methods (Pagel’s test, phylogenetic logistic regression, and D-test) to tackle this question. Two of three tests (Pagel’s test and D-test) show a clear support for haplodiploidy driving the evolution of eusociality. Experimental manipulations of data reveal that the non-significance of the logistic regression was due to the absence of haplodiploidy in aphids and termites. Overall, my study provides mixed support for the haplodiploidy hypothesis.

The kidney is known for its critical physiological functions, including regulating the level of body fluids and removal of waste products. Numerous studies have aimed to discover its formation and genetic regulation, seeking a comprehensive understanding of its characteristics. The development of the vertebrate kidney is unique among organ systems, offering distinct insights into embryonic development. It originates from a strip of tissue known as the intermediate mesoderm, developing successively from anterior to posterior to form different kidney \"stages,\" as the Pro-, Meso-, and Metanephros in Amniotes (Saxén, 1987). The pronephros, the first nephric structure in all vertebrate clades, has become a suitable model for studying the regulation of axial patterning, revealing a complex gene regulatory network governing nephrogenesis. For example, in chick embryos, Retinoic acid (RA), BMP, and Activin control the initiation of early kidney marker expression, such as Pax2 and Lim1, and establish the precise location of the developing pronephros, with a strict anterior boundary at mid-somite 6.The conservation of this gene regulatory network among vertebrates is not well understood. We employed a comparative approach, focusing on the molecular regulation and development of the pronephros in sharks, representing early gnathostomes, and lampreys, as jawless fishes. The formation of the embryonic kidney in amphioxus, (a cephalochordate, non-vertebrate organism) known as Hatschek's nephridium, was characterized and compared to the pronephros of vertebrates.My experiments (Chapter 2) demonstrated that the expression of the early kidney marker genes, Pox2 and Lim1, shares a strict anterior border in embryos of both lampreys and catsharks, at the midline of somite 6, similar to what was observed in amniotes. The expression of the Hox4 genes exhibit the same anterior pattern in the developing shark pronephros, suggesting their regulatory role in kidney marker genes expression. This spatial distribution of the pronephric field in relation to the somite number, is reminiscent of the condition in chick embryos and is likely conserved among vertebrates. In the second chapter I demonstrate that RA regulates the development of the shark pronephros, in contrast to the formation of the pronephros in lampreys and the Hatschek's nephridium of amphioxus, where RA does not affect the formation of these excretory organs. Further on, pharmacological treatments targeting additional signaling molecules (Chapter 4) revealed that the gene regulatory mechanisms are not fully conserved among the tested organisms. However, I found that Shh plays a significant role in regulating kidney marker expression in amphioxus, lampreys, and sharks. Additionally, I present evidence that BMP influences embryonic kidney development in lampreys and catsharks. My results indicate that Activin signaling might not be involved in regulating kidney marker expression in the pronephros of the catshark, but it likely plays a role in controlling kidney genes in the Hatschek's nephridium of Amphioxus These findings suggest significant evolutionary changes in the gene regulatory networks associated with pronephros development at the base of vertebrate evolution.The characterization of early kidney marker genes in sharks revealed their expression in the ventrolateral domain of somites 6-9. During development, these domains evaginate and fuse to form the pronephric duct. Experiments in lamprey embryos indicate that the first pronephros anlage is located in the ventrolateral area of the epithelial, yet undifferentiated somite. The results suggest that the pronephros in sharks and lampreys arises from a distinct somitic compartment, the nephrotome. In situ hybridizations in the cephalochordate amphioxus demonstrate that the expression of the kidney marker AmphiPax2/5/8 and the myotome marker AmphiPax3/7 overlap in the first left somite, which gives rise to Hatschek's nephridium. This finding suggests that these somite compartments in amphioxus are not strictly separated as in vertebrates and might even share common progenitor cells.My studies highlight the unique characteristics of pronephros development in early vertebrates, contrasting with conventional model organisms, and provide essential insights into the evolution of the vertebrate kidney.

Insect migration is a massive and ecologically influential phenomenon, yet there are major knowledge gaps regarding migration properties of this group. Many dragonfly species are considered migrants but only a few were thoroughly studied, none of which migrates from Europe to other areas. The Redveined Darter Sympetrum fonscolombii (Insecta: Odonata) is a common and widespread species expending its range northwards in Europe and Asia. It was recently shown, using stable Hydrogen isotope analysis, that individuals originating from the Levant migrate into West Russia during spring, but no concrete evidence of a return southward autumn migration exists. Furthermore, no systematic phenological data on any Odonata species is available from the Levant. To clarify the migratory status and natal origins of S. fonscolombii in Israel, we collected observations from various sources, and provide a first phenological description for the species in the area. Natal origins of individuals appearing on the Israeli coastline during autumn were inferred using stable Hydrogen isotopes analysis from wing samples, and a spatially explicit origins assignment. We found that the phenological pattern fits a migratory influx represented by masses recorded in autumn. The stable isotopes analysis provides the first direct evidence for a southward migration out of Europe of S. fonscolombii or any other dragonfly species, with some individuals likely originated from the extreme north parts of the species’ known range.

In Drosophila melanogaster, each of the three paralogous ABC transporters, White, Scarlet and Brown, is required for normal pigmentation of the compound eye. We have cloned the three orthologous genes from the beetle Tribolium castaneum. Conceptual translations of Tribolium white (Tcw), scarlet (Tcst), and brown (Tcbw) are 51, 48, and 32% identical to their respective Drosophila counterparts. We have identified loss-of-eye-pigment strains that bear mutations in Tcw and Tcst: the Tcw gene in the ivory (i) strain carries a single-base transversion, which leads to an E → D amino-acid substitution in the highly conserved Walker B motif, while the Tcst gene in the pearl (p) strain has a deletion resulting in incorporation of a premature stop codon. In light of these findings, the mutant strains i and p are herein renamed whiteivory (wi) and scarletpearl (stp), respectively. In addition, RNA inhibition of Tcw and Tcst recapitulates the mutant phenotypes, confirming the roles of these genes in normal eye pigmentation, while RNA interference of Tcbw provides further evidence that it has no role in eye pigmentation in Tribolium. We also consider the evolutionary implications of our findings.

Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.Bacterial DNA transfers between cells in numerous ways and becomes integrated into the genome, with diverse consequences for bacterial genomes. In this Review, Arnold, Huang and Hanage discuss the underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation.

Abstract Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature... Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation. While for more than a century, biologists have proposed this organismal feature to play an important role in evolution and the origin of novelty, the idea has remained contentious. Plasticity is found in all domains of life, but only recently has there been an increase in empirical studies. This contribution is intended as a fresh view and will discuss current and future challenges of plasticity research, and the need to identify associated molecular mechanisms. After a brief summary of conceptual, theoretical, and historical aspects, some of which were responsible for confusion and contention, I will formulate three major research directions and predictions for the role of plasticity as a facilitator of novelty. These predictions result in a four-step model that, when properly filled with molecular mechanisms, will reveal plasticity as a major factor of evolution. Such mechanistic insight must be complemented with comparative investigations to show that plasticity has indeed created novelty and innovation. Together, such studies will help develop a true developmental evolutionary biology.