bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexploitation
Authors: Cardinale Bradley J. , Primack Richard B. , Murdoch James D.
Published: September 2023

This chapter explores overexploitation, also called overharvesting, which refers to the harvesting of a renewable resource faster than it can be produced. The term applies to resources like populations of wild plants and animals, whole ecosystems, and resources that are required to sustain life. While short-term overexploitation often can be corrected, persistent overexploitation can lead to the destruction of the resource. The chapter begins with a brief overview of the history of overexploitation by humans, before reviewing the human psychology of overexploitation, pointing out the wide variety of reasons people use wild populations of plants and animals to excess. This is followed by a summary of the major types of overexploitation on both target and non-target species in a variety of habitats, including commercial exploitation, subsistence overexploitation, and recreational overexploitation. Finally, the chapter discusses theories and models for the sustainable harvest of natural resources.
Ex Situ Conservation
Authors: Cardinale Bradley J. , Primack Richard B. , Murdoch James D.
Published: September 2023

This chapter focuses on ex situ (off-site) conservation, which is the protection and management of biodiversity in artificial, human-built environments. Indeed, ex situ conservation allows wild-caught individuals to be maintained under close human supervision in facilities like zoos, aquariums, botanical gardens, or arboretums. Collections of individuals that are kept alive in artificial environments can serve as short-term buffers against extinction. However, ex situ conservation has a controversial history that has led to several criticisms and negative stereotypes. The chapter describes the role that ex situ conservation plays in local, regional, and global conservation strategies. It begins by outlining the major types of ex situ conservation facilities and what they contribute to conservation. The chapter then looks at captive-breeding programs that serve as the source of reintroductions of species to the wild.
Assimilation of Inorganic Nutrients
Authors: Taiz Lincoln , Zeiger Eduardo , Møller Ian Max , Murphy Angus
Published: September 2023

This chapter focuses on nutrient assimilation, which is the incorporation of inorganic nutrients into organic substances such as pigments, enzyme cofactors, lipids, nucleic acids, and amino acids. Assimilation of some nutrients,particularly nitrogen and sulfur, involves a complex series of biochemical reactions that are among the most energy-consuming reactions in living organisms. Assimilation of other nutrients, especially the macronutrient and micronutrient cations, involves the formation of complexes with organic compounds. The chapter outlines the primary reactions through which the major nutrients (nitrogen, sulfur, phosphate, and iron) are assimilated and discusses the organic products of these reactions. It emphasizes the physiological implications of the required energy expenditures and introduces the topic of symbiotic nitrogen fixation. Plants serve as the major conduit through which nutrients pass from slower geophysical domains into faster biological ones; the chapter thus highlights the vital role of plant nutrient assimilation in the human diet.
Photosynthesis: Physiological and Ecological Considerations
Authors: Taiz Lincoln , Zeiger Eduardo , Møller Ian Max , Murphy Angus
Published: September 2023

This chapter explores some physiological and ecological considerations concerning photosynthesis. Physiologists wish to understand the direct and indirect responses of photosynthesis to environmental factors. The dependence of photosynthetic processes on environmental conditions is also important to agronomists because plant productivity, and hence crop yield, depends strongly on prevailing photosynthetic rates in a dynamic environment. To the ecologist, photosynthetic variation among different environments is of great interest in terms of adaptation and evolution. The chapter focuses on how naturally occurring variation in light and temperature influences photosynthesis in leaves and how leaves in turn adjust or acclimate to such variation. It also describes how atmospheric CO2 influences photosynthesis, an especially important consideration in a world where CO2 concentrations are rapidly increasing as humans continue to burn fossil fuels for energy production.
Signals from Sunlight
Authors: Taiz Lincoln , Zeiger Eduardo , Møller Ian Max , Murphy Angus
Published: September 2023

This chapter discusses how sunlight also serves as a signal that regulates various developmental processes, from seed germination to fruit development and senescence. In addition, sunlight provides directional cues for plant growth as well as non-directional cues for plant movements. The receptor molecules that plants use to detect sunlight are termed photoreceptors, which undergo a conformational change when irradiated by a particular wavelength of light (perceived by the eye as colour) to initiate signaling reactions that typically involve second messengers and phosphorylation cascades collectively referred to as photoresponses. The chapter then looks at the signaling mechanisms involved in light-regulated growth and development, focusing primarily on the receptors for red light, far-red light, blue light, and UV-B radiation. It considers phytochromes, cryptochromes, and phototropins.
The Science of Plant Ecology
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter considers ecology from the perspective of terrestrial plants. It emphasizes that plant ecology is both a subset of the discipline of ecology and a mirror for the entire field. The biological science of ecology is the study of the relationships between living organisms and their environments, the interactions of organisms with one another, and the patterns and causes of the abundance and distribution of organisms in nature. The chapter then focuses on the nature of science and the scientific method. It examines how ecologists have come to their current knowledge and understanding of organisms and systems in nature. Towards the end, the chapter looks at scientific knowledge, scientific research, and observational studies. It reviews the importance of experiment, theory, measurement, analysis, and analysis to research.
Water Relations and Thermal Energy Balance
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter starts by reviewing the evolutionary history of plants on land: the story of increasing success in obtaining water, moving it to parts of the plant far from its source, and being able to reproduce in a very dry atmosphere. It points out some of the essential structures that evolved during the course of the history of land plants. Terrestrial plants not only must obtain water, but also are faced with the problem of restricting their water losses. The chapter then examines what determines water loss, and how plants control it. The chapter also shows important factors in determining leaf and plant temperatures, and what adaptations plants possess for controlling these factors so that temperatures do not get too high or too low. The chapter examines their evolutionary solutions to these interrelated problems and takes a look at the physics of water and energy exchange between plants and their environments.
Population Structure, Growth, and Decline
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter turns to discuss population dynamicsthe study of changes in numbers, composition, and the spatial dispersion of a population. Changes in population numbers are referred to as population growth, which can either increase or decrease in abundance. A key factor affecting population growth is whether those dynamics are density-dependent or density-independent (referring to individuals of the same species). The chapter then analyzes the distinction between density-dependent and density-independent factors. It focuses on the basics: density-independent population dynamics, in which density does not play a role, or its role is not considered. Because population growth is all about numbers and changing numbers, the chapter introduces some of the mathematics used to understand how plant populations grow and decline. Without the tools of mathematics, we could not understand or predict these essential things about plant populations.
Herbivory and Other Trophic Interactions
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter looks into trophic interactions of plants with a wide diversity of other organisms. Trophic interactions involve consumption of, or dependence on, energy and nutrients by one group of organisms on another group of organisms. The chapter studies how plants interact with, and defend themselves from, herbivores and pathogens, the crucial role of mycorrhizal interactions for terrestrial life, and other trophic interactions between plants and other organisms. The chapter also considers how those defenses may have evolved. The chapter then shifts to highlight the most basic of interactions: animals eating plants. It examines the effects of herbivory on individuals, populations, and communities. People have used herbivores to control populations of undesirable plantscalled biological controland the chapter investigates some of the consequences of those efforts. Finally, the chapter reviews some of the evolutionary consequences of the interactions between plants and herbivores.
Community Diversity and Structure
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter looks into the properties and characteristics of communities as a whole and some of the factors causing those properties. It first considers community patterns, then the processes that create and maintain those patterns. The chapter aims to shed a light on these questions: what determines the boundaries of a community? Are communities real entities with their own properties, or are they just random collections of individuals and populations? How predictable are the patterns? Questions of pattern like these are critical because they set the stage for the rest of the debate. Once patterns are identified, theories can be constructed to explain them. Next, the chapter investigates the ways of measuring patterns within and among communities. The issues of process focus on determining which mechanisms–such as the physiological tolerances of species, competition, herbivory, evolution, biogeography, historical contingency, and random factors influencing colonization–are most important in determining the observed patterns.
Landscapes: Pattern and Scale
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter inspects ecological patterns and processes related to spatial distributions and how they vary with spatial scale. It focuses on landscape ecology, the study of the spatial distributions of individuals, populations, and communities, and the causes and consequences of those spatial patterns. Science involves the search for patterns and for the processes that cause those patterns. What might seem to be a third activity, prediction, depends on having identified the processes that explain the observed patterns. As the chapter argues, these two aspects of science are especially apparent in landscape ecology. Finally, the chapter assesses typical pattern questions like: how are individuals, species, and communities distributed within a landscape? How many types of patches are there in a landscape? What are the sizes, shapes, and distributions of those patches? Beyond describing these patterns, the chapter aims to know the processes responsible, and the outcomes caused by these patterns.
Biomes and Physiognomy
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter stresses that our planet has a complex pattern of climates, which in turn has a major role in creating the complex pattern of vegetation and community types we find on it. Across a continent, this variation falls into regular patterns. The chapter then introduces several of these broad patterns. It begins to detail the first of these: a north-south gradient in vegetation forms due to temperature. A second major pattern is variation from west to east in response to changes in average precipitation. Ecologists divide these large-scale vegetation patterns into units called biomes. Biomes represent the greatest spatial extent at which ecologists classify vegetation. The chapter investigates these broadscale patterns and looks briefly at the major characteristics of, and threats to, the world's major biomes. It also considers plant physiognomy across the globe.
Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits
Authors: Donkpegan Armel S L , Bernard Anthony , Barreneche Teresa , Quero-García José , Bonnet Hélène , Fouché Mathieu , Le Dantec Loïck , Wenden Bénédicte , Dirlewanger Elisabeth
Published: September 2023

In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2–6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP–trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker–trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.
Prevalence, Incidence, and Predictors of Kaposi Sarcoma–Associated Herpesvirus Infection Among Young Men Who Have Sex With Men in the Southern United States
Authors: Salyards Maverick , Nijhawan Ank E , Kuo Jacky , Knights Sheena M , Lazarte Susana , Labo Nazzarena , Miley Wendell , Whitby Denise , Hwang Lu-Yu , Kornberg Anna-William , Fujimoto Kayo , Chiao Elizabeth Y
Published: September 2023

Kaposi sarcoma (KS) continues to cause substantial morbidity and mortality in populations at risk in the southern United States. Utilizing biospecimens from the Houston site of the Young Men's Affiliate Project, 351 men who have sex with men had blood tested for KS-associated herpesvirus (KSHV) IgG. Seroprevalence, seroconversion between time points, and demographic and clinical correlates were measured. KSHV prevalence was 36.7% and incidence was 8.9 per 100 person-years. Furthermore, prevalence and incidence were higher among Black individuals, people living with HIV, and those with a history of syphilis. Further research on KSHV risk may improve health disparities in KS diagnosis and outcomes.
Analysis of the Immunostimulatory Effects of Cytokine-Expressing Internal Ribosome Entry Site–Based RNA Adjuvants and Their Applications
Authors: Lee Yu-Sun , Bang Yoo-Jin , Yoo Soyeon , Park Sang-In , Park Hyo-Jung , Kwak Hye Won , Bae Seo-Hyeon , Park Hyeong-Jun , Kim Jae-Yong , Youn Sue-Bean , Roh Gahyun , Lee Seonghyun , Kwon Sung Pil , Bang Eun-Kyoung , Keum Gyochang , Nam Jae-Hwan , Hong So-Hee
Published: September 2023

Developing new adjuvants that can effectively induce humoral and cellular immune responses while broadening the immune response is of great value. In this study, we aimed to develop single-stranded RNA adjuvants expressing (1) granulocyte monocyte colony-stimulating factor or (2) interleukin 18 based on the encephalomyocarditis virus internal ribosome entry site; we also tested their efficacy in combination with ovalbumin or inactivated influenza vaccines. Notably, cytokine-expressing RNA adjuvants increased the expression of antigen-presenting cell activation markers in mice. Specifically, when combined with ovalbumin, RNA adjuvants expressing granulocyte monocyte colony-stimulating factor increased CD4+ T-cell responses, while those expressing interleukin 18 increased CD8+ T-cell responses. Cytokine-expressing RNA adjuvants further increased the frequency of polyclonal T cells with the influenza vaccine and reduced the clinical illness scores and weight loss of mice after viral challenge. Collectively, our results suggest that cytokine-expressing RNA adjuvants can be applied to protein-based or inactivated vaccines to increase their efficacy.
Migration governance in East and Southeast Asia
Authors: Chung Erin , Hollifield James F , Tian Yunchen
Published: September 2023

This article explains migration governance in East and Southeast Asia by comparing guestworker programs that have institutionalized labor migration flows between Southeast Asian countries (especially Indonesia, the Philippines, and Vietnam) and the two largest Northeast Asian recipients of labor migration, Japan and South Korea. It demonstrates how these programs have led to heightened competition for skilled labor between countries of destination, while facilitating greater migration flows between countries in Southeast and Northeast Asia. Bilateral economic agreements have engendered highly uneven, underdeveloped frameworks for protecting migrant rights and facilitating migrant integration in countries of destination. The analysis also provides insights into theories of complex interdependence and global migration governance, and shows how migration interdependence (MI) can lead to both cooperation and conflict.
A genome assembly of the Yuma myotis bat, Myotis yumanensis
Authors: Curti Joseph N , Fraser Devaughn , Escalona Merly , Fairbairn Colin W , Sacco Samuel , Sahasrabudhe Ruta , Nguyen Oanh , Seligmann William , Sudmant Peter H , Toffelmier Erin , Vazquez Juan Manuel , Wayne Robert , Shaffer H Bradley , Buchalski Michael R
Published: September 2023

The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.
AcHZP45 is a repressor of chlorophyll biosynthesis and activator of chlorophyll degradation in kiwifruit
Authors: Wu Ying-ying , Wang Ling-li , Lin Yi-lai , Li Xiang , Liu Xiao-fen , Xu Zi-Hong , Fu Bei-ling , Wang Wen-qiu , Allan Andrew C , Tu Mei-yan , Yin Xue-ren
Published: September 2023

The degradation of chlorophyll during fruit development is essential to reveal a more ‘ripe’ color that signals readiness to wild dispersers of seeds and the human consumer. Here, comparative biochemical analysis of developing fruit of Actinidia deliciosa cv. Xuxiang (‘XX’, green-fleshed) and Actinidia chinensis cv. Jinshi No.1 (‘JS’, yellow-fleshed) indicated that variation in chlorophyll content is the major contributor to differences in flesh color. Four differentially expressed candidate genes were identified: the down-regulated genes AcCRD1 and AcPOR1 involved in chlorophyll biosynthesis, and the up-regulated genes AcSGR1 and AcSGR2 driving chlorophyll degradation. Prochlorophyllide and chlorophyllide, the metabolites produced by AcCRD1 and AcPOR1, progressively reduced in ‘JS’, but not in ‘XX’, indicating that chlorophyll biosynthesis was less active in yellow-fleshed fruit. AcSGR1 and AcSGR2 were verified to be involved in chlorophyll degradation, using both transient expression in tobacco and stable overexpression in kiwifruit. Furthermore, a homeobox-leucine zipper (HD-Zip II), AcHZP45, showed significantly increased expression during ‘JS’ fruit ripening, which led to both repressed expression of AcCRD1 and AcPOR1 and activated expression of AcSGR1 and AcSGR2. Collectively, the present study indicated that different dynamics of chlorophyll biosynthesis and degradation coordinate the changes in chlorophyll content in kiwifruit flesh, which are orchestrated by the key transcription factor AcHZP45.
How numerical treatments of the transition region modify energy flux into the solar corona
Authors: Howson T A , Breu C
Published: September 2023

The large temperature gradients in the solar transition region present a significant challenge to large-scale numerical modelling of the Sun’s atmosphere. In response, a variety of techniques have been developed which modify the thermodynamics of the system. This sacrifices accuracy in the transition region in favour of accurately tracking the coronal response to heating events. Invariably, the modification leads to an artificial broadening of the transition region. Meanwhile, many contemporary models of the solar atmosphere rely on tracking energy flux from the lower atmosphere, through the transition region and into the corona. In this paper, we quantify how the thermodynamic modifications affect the rate of energy injection into the corona. We consider a series of one-dimensional models of atmospheric loops with different numerical resolutions and treatments of the thermodynamics. Then, using Alfvén waves as a proxy, we consider how energy injection rates are modified in each case. We find that the thermodynamic treatment and the numerical resolution significantly modify Alfvén traveltimes, the eigenfrequencies and eigenmodes of the system, and the rate at which energy is injected into the corona. Alarmingly, we find that the modification of the energy flux is frequency dependent, meaning that it may be difficult to compare the effects of different velocity drivers on coronal heating if they are imposed below an under-resolved transition region, even if the sophisticated thermodynamic adaptations are implemented.
Spatially resolved spectroscopic investigation of the born-again planetary nebula A 78
Authors: Montoro-Molina B , Guerrero M A , Toalá J A
Published: September 2023

We present the analysis of spatially resolved spectroscopic observations of the born-again planetary nebula (PN) A 78 that are used to investigate the chemistry and physical properties of its three main morphological components, namely the inner knots, its eye-like structure, and the low surface-brightness outer nebula. The H-poor chemical abundances of the inner knots confirm the born-again nature of A 78, with an N/O abundances ratio consistent with the predictions of very late thermal pulses (VLTP). On the other hand, the high Ne/O is not expected in VLTP events, which prompts a possible different evolutionary path may be involving a binary system. The low N/O ratio and He/H abundances of the outer shell are indicative of a low-mass progenitor, whereas the chemical abundances of the eye-like structure, which results from the interaction between the H-poor born-again material and the outer nebula, evidence their mixture. Unlike previous works, the extinction is found to be inhomogeneous, being much higher towards the H-poor inner knots, where the presence of large amounts of C-rich dust has been previously reported. Dust-rich material seems to diffuse into outer nebular regions, resulting in zones of enhanced extinction.
A re-assessment of SpArcFiRe’s performance on toy spiral galaxies
Authors: Portman Matthew E , Mesforoush Sahel , Hayes Wayne B
Published: September 2023

Recently, a study (H&T in this work) compared the pitch angle measurements of several methods on toy spiral galaxies. They claimed that their method outperformed the other methods. In particular, they claimed that our method, SpArcFiRe, either failed completely or produced erroneous results on many of their toy galaxies. In this paper, we assess the validity of that claim with respect to: (1) their toy models as realistic approximations of galaxies, and (2) the handling of SpArcFiRe’s parameters to correctly trace the arms of the toy galaxies. We demonstrate that the structure displayed in their toy galaxies deviates significantly from those of real galaxies. Given that SpArcFiRe was designed for and tested against hundreds of thousands of images of real galaxies, SpArcFiRe could not have been expected to work well with default parameters on H&T’s unrealistic toy galaxies. We then review the parameters that affected SpArcFiRe’s ability to measure pitch angles in the toy galaxies, and show that with minor parameter adjustments, SpArcFiRe easily measures the pitch angles of the toy galaxies with mean error less than 1° and maximum error less than 4°, completely eliminating the failures and outliers discussed by H&T.
Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods
Authors: du Plessis Sarah J , Blaxter Mark , Koepfli Klaus-Peter , Chadwick Elizabeth A , Hailer Frank
Published: September 2023

Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated “stronghold” populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s–1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
Ovarian stimulation with excessive FSH doses causes cumulus cell and oocyte dysfunction in small ovarian reserve heifers
Authors: Karl Kaitlin R , Schall Peter Z , Clark Zaramasina L , Ruebel Meghan L , Cibelli Jose , Tempelman Robert J , Latham Keith E , Ireland James J
Published: September 2023

Excessive FSH doses during ovarian stimulation in the small ovarian reserve heifer (SORH) cause premature cumulus expansion and follicular hyperstimulation dysgenesis (FHD) in nearly all ovulatory-size follicles with predicted disruptions in cell-signaling pathways in cumulus cells and oocytes (before ovulatory hCG stimulation). These observations support the hypothesis that excessive FSH dysregulates cumulus cell function and oocyte maturation. To test this hypothesis, we determined whether excessive FSH-induced differentially expressed genes (DEGs) in cumulus cells identified in our previously published transcriptome analysis were altered independent of extreme phenotypic differences observed amongst ovulatory-size follicles, and assessed predicted roles of these DEGs in cumulus and oocyte biology. We also determined if excessive FSH alters cumulus cell morphology, and oocyte nuclear maturation before (premature) or after an ovulatory hCG stimulus or during IVM. Excessive FSH doses increased expression of 17 cumulus DEGs with known roles in cumulus cell and oocyte functions (responsiveness to gonadotrophins, survival, expansion, and oocyte maturation). Excessive FSH also induced premature cumulus expansion and oocyte maturation but inhibited cumulus expansion and oocyte maturation post-hCG and diminished the ability of oocytes with prematurely expanded cumulus cells to undergo IVF or nuclear maturation during IVM. Ovarian stimulation with excessive FSH is concluded to disrupt cumulus cell and oocyte functions by inducing premature cumulus expansion and dysregulating oocyte maturation without an ovulatory hCG stimulus yielding poor-quality cumulus–oocyte complexes that may be incorrectly judged morphologically as suitable for IVF during ART.
Tensin 1 regulated by hepatic leukemia factor represses the progression of prostate cancer
Authors: Zhou Hao , Wang Fang
Published: September 2023

Hepatic leukemia factor (HLF), a transcription factor, is dysregulated in many cancers. This study investigates the function of HLF in prostate cancer (PCa) and its relation to tensin 1 (TNS1). Clinical tissues were collected from 24 PCa patients. Duke University 145 (DU145) and PC3 cells overexpressing HLF were established. HLF signaling was downregulated in PCa tissues compared to adjacent tissues and in DU145 and PC3 cells compared to prostate epithelial cells RWPE-1 or prostate stromal cells (WPMY-1). PCa cell lines with overexpression of HLF had reduced proliferative, migratory, and invasive activity, increased apoptosis, and cell mitosis mostly in the G0/G1 phase. HLF induced the TNS1 transcription to activate the p53 pathway. Depletion of TNS1 reversed the anti-tumor effects of HLF on PCa cells and tumor growth and metastasis in vivo. In summary, our findings suggest that HLF suppressed PCa progression by upregulating TNS1 expression and inducing the p53 pathway activation, which might provide insights into novel strategies for combating PCa.
Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation
Authors: Wegrzyn Katarzyna , Oliwa Monika , Nowacka Marzena , Zabrocka Elżbieta , Bury Katarzyna , Purzycki Piotr , Czaplewska Paulina , Pipka Justyna , Giraldo Rafael , Konieczny Igor
Published: September 2023

For DNA replication initiation in Bacteria, replication initiation proteins bind to double-stranded DNA (dsDNA) and interact with single-stranded DNA (ssDNA) at the replication origin. The structural–functional relationship of the nucleoprotein complex involving initiator proteins is still elusive and different models are proposed. In this work, based on crosslinking combined with mass spectrometry (MS), the analysis of mutant proteins and crystal structures, we defined amino acid residues essential for the interaction between plasmid Rep proteins, TrfA and RepE, and ssDNA. This interaction and Rep binding to dsDNA could not be provided in trans, and both are important for dsDNA melting at DNA unwinding element (DUE). We solved two crystal structures of RepE: one in a complex with ssDNA DUE, and another with both ssDNA DUE and dsDNA containing RepE-specific binding sites (iterons). The amino acid residues involved in interaction with ssDNA are located in the WH1 domain in stand β1, helices α1 and α2 and in the WH2 domain in loops preceding strands β1’ and β2’ and in these strands. It is on the opposite side compared to RepE dsDNA-recognition interface. Our data provide evidence for a loop-back mechanism through which the plasmid replication initiator molecule accommodates together dsDNA and ssDNA.
A multi-scale expression and regulation knowledge base forEscherichia coli
Authors: Lamoureux Cameron R , Decker Katherine T , Sastry Anand V , Rychel Kevin , Gao Ye , McConn John Luke , Zielinski Daniel C , Palsson Bernhard O
Published: September 2023

Transcriptomic data is accumulating rapidly; thus, scalable methods for extracting knowledge from this data are critical. Here, we assembled a top-down expression and regulation knowledge base for Escherichia coli. The expression component is a 1035-sample, high-quality RNA-seq compendium consisting of data generated in our lab using a single experimental protocol. The compendium contains diverse growth conditions, including: 9 media; 39 supplements, including antibiotics; 42 heterologous proteins; and 76 gene knockouts. Using this resource, we elucidated global expression patterns. We used machine learning to extract 201 modules that account for 86% of known regulatory interactions, creating the regulatory component. With these modules, we identified two novel regulons and quantified systems-level regulatory responses. We also integrated 1675 curated, publicly-available transcriptomes into the resource. We demonstrated workflows for analyzing new data against this knowledge base via deconstruction of regulation during aerobic transition. This resource illuminates the E. coli transcriptome at scale and provides a blueprint for top-down transcriptomic analysis of non-model organisms.
TTD: Therapeutic Target Database describing target druggability information
Authors: Zhou Ying , Zhang Yintao , Zhao Donghai , Yu Xinyuan , Shen Xinyi , Zhou Yuan , Wang Shanshan , Qiu Yunqing , Chen Yuzong , Zhu Feng
Published: September 2023

Target discovery is one of the essential steps in modern drug development, and the identification of promising targets is fundamental for developing first-in-class drug. A variety of methods have emerged for target assessment based on druggability analysis, which refers to the likelihood of a target being effectively modulated by drug-like agents. In the therapeutic target database (TTD), nine categories of established druggability characteristics were thus collected for 426 successful, 1014 clinical trial, 212 preclinical/patented, and 1479 literature-reported targets via systematic review. These characteristic categories were classified into three distinct perspectives: molecular interaction/regulation, human system profile and cell-based expression variation. With the rapid progression of technology and concerted effort in drug discovery, TTD and other databases were highly expected to facilitate the explorations of druggability characteristics for the discovery and validation of innovative drug target. TTD is now freely accessible at: https://idrblab.org/ttd/.
Comparing post-traumatic stress severity in professional and volunteer Australian firefighters
Authors: Counson I , Sanatkar S , Knight A , Lawrence D , Harvey S B
Published: September 2023

Background

While extensive research has highlighted increased risk for post-traumatic stress disorder (PTSD) in firefighters, previous research has yielded mixed results regarding the role of work status (professional versus volunteer) in the development of psychopathological symptoms.

Aims

To explore the predictive strength of work status on PTSD or post-traumatic stress symptom severity in a large sample of professional (PFFs) and volunteer (VFFs) Australian firefighters exposed to operational work-related trauma.

Methods

The stratified random sample comprised 1317 PFFs (n = 1148 (87%) males and 13%, n = 169 (13%) females) and 898 VFFs (n = 744 (83%) males and n = 154 (17%) females) who reported having experienced trauma while working or volunteering. Participants completed demographic, health and work-related questions and mental health measures of stress, trauma, PTSD, social support and use of mental health prevention programmes.

Results

The results revealed a significant relationship between work status and PTSD, with PFFs reporting higher levels of PTSD symptom severity compared to VFFs. This association persisted after controlling for demographics, health, stress away from work, social support and use of organizational mental health support programmes (debriefing and face-to-face training for mental and physical self-care).

Conclusions

This study suggests the importance of work status in PTSD amongst Australian firefighters exposed to operational trauma. Future research is needed to substantiate our findings and examine why PFFs may be more prone to developing PTSD. Implications for the provision of mental health programmes offered by fire organizations to their members are discussed.
The SYP123–VAMP727 SNARE complex delivers secondary cell wall components for root hair shank hardening in Arabidopsis
Authors: Hirano Tomoko , Ebine Kazuo , Ueda Takashi , Higaki Takumi , Watanabe-Nakayama Takahiro , Konno Hiroki , Takigawa-Imamura Hisako , Sato Masa H
Published: September 2023

The extended tubular shape of root hairs is established by tip growth and concomitant hardening. Here, we demonstrate that a syntaxin of plants (SYP)123–vesicle-associated membrane protein (VAMP)727-dependent secretion system delivers secondary cell wall components for hardening the subapical zone and shank of Arabidopsis (Arabidopsis thaliana) root hairs. We found increased SYP123 localization at the plasma membrane (PM) of the subapical and shank zones compared with the tip region in elongating root hairs. Inhibition of phosphatidylinositol (PtdIns)(3,5)P2 production impaired SYP123 localization at the PM and SYP123-mediated root hair shank hardening. Moreover, root hair elongation in the syp123 mutant was insensitive to a PtdIns(3,5)P2 synthesis inhibitor. SYP123 interacts with both VAMP721 and VAMP727. syp123 and vamp727 mutants exhibited reduced shank cell wall stiffness due to impaired secondary cell wall component deposition. Based on these results, we conclude that SYP123 is involved in VAMP721-mediated conventional secretion for root hair elongation as well as in VAMP727-mediated secretory functions for the delivery of secondary cell wall components to maintain root hair tubular morphology.
The chest CT signs for pulmonary veno-occlusive disease correlate with pulmonary haemodynamics in systemic sclerosis
Authors: Moriya Haruka , Kato Masaru , Hisada Ryo , Ninagawa Keita , Tada Maria , Sakiyama Kodai , Yasuda Mitsutaka , Kono Michihito , Fujieda Yuichiro , Amengual Olga , Kikuchi Yasuka , Tsujino Ichizo , Sato Takahiro , Atsumi Tatsuya
Published: September 2023

Objectives

Pulmonary arterial hypertension associated with systemic sclerosis (PAH-SSc) sometimes accompanies pulmonary veno-occlusive disease (PVOD). We aimed to reveal the relationship between clinical signs of PVOD and severity of pulmonary vasculopathy in SSc.

Methods

This study included 52 consecutive SSc patients who had pulmonary haemodynamic abnormalities [mean pulmonary arterial pressure (mPAP) >20 mmHg, pulmonary vascular resistance >2 WU or pulmonary artery wedge pressure (PAWP) >15 mmHg]. A chest CT scan was evaluated in all patients. Patients were divided into two groups, the 0–1 group and the 2–3 group, according to the number of chest CT signs for PVOD, including mediastinal lymph node enlargement, thickened interlobular septal wall and ground glass opacity. Pulmonary haemodynamics, echocardiography and MRI-based cardiac function, pulmonary function and serum biomarkers were compared between the two groups.

Results

Mediastinal lymph node enlargement, thickened interlobular septal wall and ground glass opacity were observed in 11 (21%), 32 (62%) and 11 (21%) patients, respectively. The 2–3 group (n = 15) had higher mPAP (P = 0.02) but lower diffusing capacity of carbon monoxide (DLCO)/alveolar volume (P = 0.02) compared with the 0–1 group (n = 37). Other parameters, including PAWP, cardiac output, left ventricular ejection fraction, left atrial diameter, forced vital capacity, brain natriuretic peptide and Krebs von den Lunge-6 were not different between the two groups.

Conclusions

The CT signs for PVOD had a positive correlation with mPAP but a negative correlation with DLCO in SSc patients, indicating that PAH-SSc may reflect a spectrum of pulmonary vascular disease that ranges from the pulmonary artery to the vein.
Tolerability and comparative effectiveness of TNF, IL-17 and IL-23(p19) inhibitors in psoriatic arthritis: a target trial emulation study
Authors: Stisen Zara R , Nielsen Sabrina M , Skougaard Marie , Mogensen Mette , Jørgensen Tanja Schjødt , Dreyer Lene , de Wit Maarten , Christensen Robin , Kristensen Lars Erik
Published: September 2023

Objectives

To compare the tolerability and effectiveness of two different classes of biological DMARDs [IL-17 and IL-23(p19) inhibitors, IL-17i and IL-23(p19)i] relative to TNF inhibitors (TNFi) regarding the drug survival rates and treatment outcomes in patients with PsA.

Methods

We emulated a target trial on comparative effectiveness using observational data from a prospective cohort study based on the Parker Institute’s PsA cohort (the PIPA cohort). All patients underwent interview and a clinical examination programme at baseline and at follow-up visits at 4 and 12 months. The primary endpoint, drug survival, was assessed up to 12 months from baseline. We estimated hazard ratios from proportional hazards model and used propensity score adjustment in an attempt to deconfound and emulate a random treatment assignment.

Results

We included a total of 109 patients in the intention-to-monitor population at baseline initiating either TNFi (75 patients), IL-17i (26 patients) or IL-23(19)i (8 patients). Hazard ratios in the propensity adjusted model comparing IL-17i and IL-23(p19)i with TNFi were 1.36 (95% CI 0.59–3.14) and 0.56 (95% CI 0.10–3.24), respectively. TNFi and IL-17i had comparable effects regarding response rates and changes in clinical outcomes after 12 months, whereas IL-23(p19)i tended to perform better overall.

Conclusion

No decisive differences between drugs were observed at group level regarding drug survival and clinical outcomes after 12 months. TNFi, IL-17i and IL-23(p19)i may all be considered equally effective in the treatment of patients with PsA, advocating for investigating more in personalized treatment strategies.
Cognitive Health Disparities by Race and Ethnicity: The Role of Occupational Complexity and Occupational Status
Authors: Sheftel Mara Getz , Goldman Noreen , Pebley Anne R , Pratt Boriana , Park Sung S
Published: September 2023

Disparities in older age cognitive health by race/ethnicity persist even after controlling for individual-level indicators of childhood and adult socioeconomic status. High levels of labor market segregation mean that Black and Latino workers, on average, may not have the same exposure to jobs involving complex work with data and people as their White counterparts, aspects of work that appear to be protective of older adult cognition. However, the role of variation in exposure to occupational complexity by race/ethnicity remains understudied as an explanation for cognitive disparities at older ages. This paper uses detailed work histories constructed from the Health and Retirement Study (HRS) Occupation and Industry life history data to understand the role of occupational complexity in the development of dementia at older ages. It also addresses a conjecture that complexity reflects occupational status. Findings highlight that: (a) occupations involving complex work with data during working ages may be protective against dementia at older ages, potentially contributing to the differentials in dementia prevalence for Black, Latino, and White workers, and (b) occupational complexity reflects occupational status. This research increases understanding of the implications of labor market segregation for cognitive health disparities by race/ethnicity.
Effect of Transforaminal Epidural Corticosteroid Injections in Acute Sciatica A Randomized Controlled Trial
Authors: Ter Meulen Bastiaan C. , van Dongen Johanna M. , Maas Esther , van de Vegt Marinus H. , Haumann Johan , Weinstein Henry C. , Ostelo Raymond
Published: September 2023

Objective:

Transforaminal epidural steroid injections (TESIs) are widely administered for sciatica. The aim of this trial was to evaluate the effectiveness of TESIs in patients with acute sciatica (<8 wk).

Methods:

This study was conducted in two Dutch hospitals. Participants (n=141) were randomly assigned to: 1) usual care and TESI of 1ml of 40mg/ml Methylprednisolone plus 1ml of 0.5% Levobupivacaine (intervention 1); 2) usual care and transforaminal epidural injection with 1 ml of 0.5% Levobupivacaine and 1ml NaCl 0.9% (intervention 2); 3) usual care consisting of oral pain medication with or without physiotherapy (control). Co-primary outcomes were back- and leg pain intensity, physical functioning and recovery measured during 6-month follow-up.

Results:

There were no significant mean differences in co-primary outcomes between groups during follow-up, except for leg pain when comparing intervention group 1 with control (-0.96 95%CI:-1.83 to -0.09). For secondary outcomes, some significant between group differences were found for treatment satisfaction and surgery, but only when comparing intervention group 2 to control. Post-hoc analyses showed a significant difference in response (50% improvement of leg pain [yes/no]) between intervention 1 and the control group at 3 months and that both intervention groups used less opioids.

Discussion:

Except for a statistically significanteffect of TESI on leg pain for patients with acute sciatica compared to usual care, there were no differences in co-primary outcomes. Nonetheless, transforaminal epidural injections seem to be associated with less opioid use, which warrants further exploration.