bluuebunny/crossref_metadata_2025 huggingface dataset:
Glycosylphosphatidylinositol-anchored proteins and their phospholipases
Authors: Low Martin G
Published: November 2023

A large number of eukaryotic cell-surface proteins are covalently linked to glyco-sylphosphatidylinositol (GPI). A GPI molecule consists of a short glycan chain containing four sugar residues glycosidically linked to the 6-OH of a phosphatidylinositol molecule (see Fig. 1). The other, non-reducing end of the glycan chain bears a phosphodiester-linked ethanolamine residue. A GPI molecule is attached post-translationally to proteins via an amide linkage between the terminal phospho-ethanolamine and the carboxyl group of the C-terminal amino acid. The lipid moiety of the GPI is inserted into the lipid bilayer and is responsible for anchoring the protein to the cell membrane. Proteins can utilize other types of lipid anchor, involving prenyl, palmitoyl, or myristoyl groups but, in eukaryotic cells, GPI is the only lipid that can anchor proteins to the cell surface. The GPI anchor is susceptible to cleavage by several phospholipases that are distinct from those involved in the hydrolysis of intracellular inositol phospholipids. Cleavage of the anchor by these phospholipases releases GPI-anchored proteins from the membrane. The relatively complex structure of the GPI molecule and evolutionary conservation of its major features suggest that the GPI anchor confers additional properties on the proteins besides attachment to the cell surface. GPI molecules and GPI-anchored proteins have been proposed to play a role in cellular signalling as well as targeting proteins to particular regions of the cell surface. However, the mechanism and physiological significance of these additional functions is uncertain.
Assessment of DNA damage cell cycle checkpoints in G1 and G2 phases of mammalian cells
Authors: O’connor Patrick M , Jackman Joany
Published: November 2023

Cell cycle progression is normally tightly regulated such that one cell cycle event does not occur unless the previous cell cycle event has been completed. For example, mammalian cells do not normally enter mitosis while DNA replication is on-going, and cells in mitosis do not normally exit mitosis unless the spindle apparatus is correctly aligned with all the chromosomes. This dependency is controlled by a series of negative-feedback control systems that are called checkpoints (1-4). These checkpoints are being studied in a variety of organisms from yeast to human, and a growing number of studies implicate defective checkpoint control systems in the emergence and evolution of human cancer. One example is the p53 tumour suppressor, the most commonly mutated gene in human cancer (1, 2). p53 is essential for the arrest of cell cycle progression in the 01 phase following DNA damage. Loss of p53 function prevents this arrest mechanism from being activated and also sub dues or blocks the induction of apoptosis in DNA damaged cells. In addition, p53 has influences on other cell cycle checkpoints (02 and M phase) which act together to ensure the fidelity of DNA replication and chromosome segregation. Such actions help to explain why there is a markedly increased likelihood of cancer in mice deficient for p53 function (5).
Human leukaemia cells as a model differentiation system
Authors: Moore Dorothy C , Studzinski George P
Published: November 2023

Cell differentiation usually proceeds at the same time as cessation of cell proliferation, andin vitrosystems for cell differentiation provide excellent models to study orderly down-regulation of growth-related cellular activities. Many such models are available, and these are illustrated in this volume with reference to systems frequently used to study differentiation of human malig-nant cells. Differentiation of colon cancer cells is described in Chapter 12, of human prostate cancer in Chapter 13, and of human leukaemia in this chapter.
Active microelectronic arrays for DNA hybridization analysis
Authors: Heller Michael j. , Tu Eugene , Holmsen Anita
Published: November 2023

Miniaturized DNA arrays, DNA chips, and lab on a chip devices represent a new area of high technology that will revolutionize the way many important molecular biological-type experiments, assays, and tests are performed in both research and clinical diagnostic laboratories. The development of these new technologies has been brought about by a synergistic combination of diverse disciplines which include: microfabrication, organic chemistry, molecular biology, and genetics. In particular, many of these devices and technologies take advantage of sophisticated microfabrication processes developed by the semiconductor industry over the last 40 years.
Assaying binding and covalent modifications of cytoskeletal proteins
Authors: Ampe Christophe , Vandekerckhove Joël
Published: November 2023

Cytoskeletal dynamics are essential for cell survival. The microfilament system is one of the major players in cell motility processes. It exerts force for movement either by the action of molecular motors on relatively stable filaments or by dynamic turnover of actin filaments. In the latter case processes such as filament polymerization, depolymerization. and bundling are regulated in a temporal and spatial manner, governed by actin-binding proteins. The complexity of the actin system arises from the multitude of actin-binding proteins, often with partly overlapping activities, displaying multiple functions or effects on actin polymerization, depending on the intracellular environment. Therefore, detailed biochemical studies of individual actin-binding proteins and their interaction with actin or with regulatory ligands are necessary to understand cellular motility phenomena. The field is now slowly progressing towards in vitro studies with more than one actin-binding protein, because it is dear that in cells these proteins either compete with each other or have additive or co-operative effects on aetin reorganization.
Ras-related GTPases and the cytoskeleton
Authors: Ridley Anne J , Flinn Helen M
Published: November 2023

The Ras supcrfamily or GTPascs all hind GTP, and can hydrolyse GTP to yield Ci DP. They act as molecular witches in cells and are active when bound to GTP, assuming a conformation which allows them to interact with their downstream target proteins. In the GDP-bound conformation they no longer hind to most target proteins (I, 2). Under physiological conditions, exchange of guanine nucleotides on the GTPases is very slow and is catalysed by exchange factors, while GTP hydrolysis is catalysed by GTPase activating proteins (GAPs) (Figure 1).
Overview of apoptosis
Authors: Studzinski George P
Published: November 2023

When cells receive mixed signals for growth they usually die. For instance, when the developmental programme requires cell division but external growth signals are lacking, or when a growth-related gene such as c-myc is highly expressed but the cellular environment has insufficient nutrient content, or a toxic xenobiotic is present, the cell dies by a process termed apoptosis. Although there are differences in the phenomena observed during the apoptotic sequence of events, depending on the cell type, and agent or circumstance which initiates the cell’s demise, there are morphological and biochemical similarities which suggest that these are variants of the same biological process, designed to control the size of cell populations.
Sphingolipids as messengers of cell death
Authors: Jenkins Gary M , Hannun Yusuf A
Published: November 2023

This chapter discusses the most commonly used methods for the study of sphingolipids in their role as messengers of cell death. A basic review of sphingolipids and the role they play in apoptosis is given. The rest of the chapter outlines the methods used for the study of sphingolipids and the enzymes relevant to the sphingomyelin (SM) cycle. Each method is described with full experimental details, and emphasis is given to one or two protocols used for the study of each class of sphingolipids and relevant enzymes.
Multiple alignments for structural, functional, or phylogenetic analyses of homologous sequences
Authors: Duret L , Abdeddaim S
Published: November 2023

Understanding the structure, function and evolution of genes is one of the main goals of genome sequencing projects. Classically, gene function has been investigated experimentally through the analysis of mutant phenotypes. More recently, comparative analysis of homologous sequences has proved to be a very efficient approach to study gene function (this approach has been coined ‘comparative genomics’ or ‘phylogenomics’). Indeed, the evolution of living organisms maybe considered as an ongoing large-scale mutagenesis experiment. For more than three billion years, genomes have continuously undergone mutations (substitutions, insertion, deletions, recombination, and so on). Deleterious mutations are generally rapidly eliminated by natural selection, while mutations that have no phenotypic effect (neutral mutations) may, by random genetic drift, eventually become fixed in the population. Globally, advantageous mutations are very rare, and hence residues that are poorly conserved during evolution generally correspond to regions that are weakly constrained by selection (l). Thus, studying mutation patterns through the analysis of homologous sequences is useful not only to study evolutionary relationships between sequences, but also to identify structural or functional constraints on sequences (DNA, RNA, or protein).
Introduction to basic principles
Authors: Freshney R Ian
Published: November 2023

Cell culture has become an indispensable technology in many branches of the life sciences. It provides the basis for studying the regulation of cell proliferation, differentiation and product formation in carefully controlled conditions, with processes and analytical tools which are scalable from the level of the single cell to in excess of 10 kg wet weight of cells. Cell culture has also provided the means to define almost the entire human genome, and to dissect the pathways of intracellular and intercellular signalling which ultimately regulate gene expression. From its ancestry in developmental biology and pathology, this discipline has now emerged as a tool for molecular geneticists, immunologists, surgeons, bioengineers, and manufacturers of phannaceuticals, while still remaining a fundamental tool to the cell biologist, whose input is vital for the continuing development of the technology.
Cell polarity in yeast
Authors: BÄHler JÜrg , Peter Matthias
Published: November 2023

Eukaryotic cells respond to intracellular and extracellular cues to direct cell growth and division. Selecting sites of polarized growth and division is crucial for the development of both unicellular and multicellular organisms. The two yeasts Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast) have rigid cell walls. Cellular polarization targets secretion of cell wall and other materials to restricted areas in the cell. As a result, cell polarity in these yeasts directly underlies cellular morphogenesis. Both budding and fission yeast establish cell polarity at several stages for growth, cytokinesis, mating, and sporulation. Thus, they are useful model organisms for studying various aspects of cell polarity. In recent years, many regulatory and cytoskeletal components important for directing and establishing polarity have been identified, and molecular mechanisms underlying polarity development in yeast have been elucidated. Key signalling pathways that regulate polarization during the cell cycle and mating response have been described. Since many of the components important for polarized cell growth are conserved in other organisms, the basic mechanisms mediating cell polarity are likely to be universal among eukaryotes.
Cell polarity in algae and vascular plants
Authors: Fowler John E
Published: November 2023

Due to the presence of the plant cell wall, the morphogenesis and physiology of plant cells and animal cells are under different constraints. Plant cells are immobile, and fixed in relation to their neighbours; morphogenetic changes in the plant cannot occur by the cellular migration mechanisms common during animal development. Furthermore, modificati6n of plant cell shape must occur through modification of the surrounding cell wall. Thus, mechanisms that allow co-ordination and expression of morphogenetic changes in plants are coupled with mechanisms that regulate growth, both by expansion and division of cells.
Genetic analysis of intrinsically asymmetrical cell division
Authors: Piano Fabio , Kemphues Kenneth
Published: November 2023

Intrinsically asymmetrical cell division is a major mechanism for generating cell diversity. In this process, referred to simply as asymmetrical division in this chapter, cytoplasmic and cortical asymmetries within a mother cell combine with an oriented cell division to produce daughter cells with different cytoplasmic components and consequently different cell fates (1). As illustrated in Fig. 1, there are three processes that contribute to asymmetrical cell divisions: (1) establishment of polarity; (2) localization of determinants; (3) oriented cell division.
Polarized exocytosis: targeting vesicles to specific dotnains on the plastna membrane
Authors: Brennwald Patrick , Adamo Joan
Published: November 2023

The ability to deliver newly synthesized proteins and lipids to discrete sites on the cell surface allows cells to grow asymmetrically (i.e. tall and thin versus round), to release morphogens on a discrete side of a cell layer during early embryonic development, and to carry out a variety of other processes. The involvement of delivery events is particularly apparent during asymmetrical growth. This is because the ability of the surface to expand requires the addition of new phospholipids and integral membrane proteins, which are the building blocks that allow cell-surface growth. Lipids and integral membrane proteins are extremely hydrophobic in nature and thus they cannot reach the plasma membrane by simple diffusion through the cytoplasm. Instead, they are brought to the cell surface in the form of membranous transport vesicles. These transport or secretory vesicles contain materials first synthesized in the endoplasmic reticulum, and then delivered to the Golgi apparatus, within which the secretory vesicles themselves are derived. These post-Golgi secretory vesicles represent the last stage of the exocytic pathway and their fusion with the cell surface is often referred to is exocytosis. In this chapter, we will discuss the mechanisms and machinery that regulate the delivery and fusion of secretory vesicles with specific sites on the plasma membrane, the process of polarized exocytosis.
Determination of active site concentration
Authors: Martin Mark T
Published: November 2023

Enzyme quantitation methods vary widely in complexity and reliability (Table 1). Methods that assume an enzyme is homogeneous and fully active (gravimetric or total protein assays) are far less reliable than methods that measure the concentration of functional enzyme (active site titrations1 and substrate turnover rate assays). Of those methods that measure functional enzyme, active site titrations tend to be more reliable than activity assay methods. In contrast to activity assay methods, titrations do not require primary standards of 100% pure and active enzyme and are less likely to be affected by small variations in assay conditions (pH, ionic strength, temperature, etc.).
High throughput screening – considerations for enzyme assays
Authors: Hayes David , Mellor Geoff
Published: November 2023

The rapidly increasing number of potential therapeutic targets is leading the pharmaceutical industry to radically alter its drug discovery strategy (for reviews, see 1–6). For these targets, there is often little or no structural information available for the rational design of putative drug candidates. Additionally, there is a desire to obtain ‘lead’ molecules of novel structure, to avoid patent infringement of known inhibitors. One approach to address these issues is to assay large numbers of compounds against the target, either in a random or sometimes targeted fashion, a process termed high throughput screening (HTS). The precise nature of these targets varies widely; for example they can be receptor–ligand, protein–protein, protein–carbohydrate, DNA and RNA interactions, ion-channels or enzymes. For this chapter we will consider only enzyme targets and will discuss the requirements for successful assay development and validation and subsequent screening. Details of two example assays are given, along with a snapshot of automation required to facilitate the process.
Statistical analysis of enzyme kinetic data
Authors: Cornish-Bowden Athel
Published: November 2023

All serious kinetic investigations of enzymes include some data analysis, and the methods used can be classified into three categories: (i) graphical analysis; (ii) best-fit analysis with general-purpose commercial packages; (iii) best-fit analysis with specialized programs designed with enzyme kinetic experiments in mind. The near-universal availability of small computers—a major change from the context in which the chapter corresponding to this one in the first edition of this book (1) was written—has greatly increased the use of the second of these approaches, but the others continue to be widely used.
Gel electrophoresis of proteins
Authors: Gartin David E
Published: November 2023

At one time or another during the course of protein analysis or purification, researchers are likely to make use of gel electrophoresis. All laboratories working with proteins have some capability for carrying out gel electrophoresis and all researchers have at least rudimentary knowledge of the technique. Gel electrophoresis can provide information about the molecular weights and charges of proteins, the subunit structures of proteins, and the purity of a particular protein preparation. It is relatively simple to use and it is highly reproducible. The most common use of gel electrophoresis is the qualitative analysis of complex mixtures of proteins. Microanalytical methods and sensitive, linear image analysis systems make gel electrophoresis popular for quantitative and preparative purposes as well.
Fluorescence-based iber-optic biosensors
Authors: Walt David R , Schauer Caroline L , Stitzel Shannon E , Fleming Michael S , Epstein Jason R
Published: November 2023

This chapter describes optical biosensors that combine analyte-sensitive indicators with optical fibers for detecting chemical and biological species. Fiber-optic biosensors are more versatilebecause they are flexible in terms of their platform design and signal transduction. Optical transduction mechanisms include fluorescence, absorbance, and reflectance. Using these mechanisms, sensors can be designed to exploit optically detectable differences in intensity, lifetime, spectral shape, polarization, and wavelength (1). Optical fibers come in a range of lengths and diameters, and can be adapted for either single-or multianalyte detection, and can incorporate a variety of sensing chemistries.
Primary culture and the establishment of cell lines
Authors: MacDonald Caroline
Published: November 2023

A wide range of cultured animal cell lines has been described in the literature and is available from tissue culture collections such as the European Collection of Cell Cultures (ECACC) in the UK and the American Type Culture Collection (ATCC) in the USA (see Appendix 2). These lines are from different animal species, including humans, and increasingly insect cell lines have become available as interest grows in the baculovirus expression system for the production of proteins. Such lines, while providing a valuable resource and being appropriate for many uses, are not suitable for all purposes. In this situation the scientist may consider establishing his or her own primary culture and, if feeling particularly adventurous and optimistic, trying to isolate a new cell line. The aim of this chapter is to describe some of the approaches which are available and to indicate, wherever possible, how to go about deciding which method to use.
Detection and population analysis of IL-1 and TNF gene polymorphisms
Authors: Di Giovine Francesco S , Camp Nicola J , Cox Angela , Chaudhary Adeel G , Sorrell Julian A , Crane Alison , Duff Gordon W
Published: November 2023

The pro-inflammatory cytokines IL-1 and 1NF-a mediate inflammatory responses by attracting, and activating, white blood cells to tissues, and stimulating the secretion of other lymphocytotropic cytokines and catabolic enzymes (1, 2). In acute infection the inflammatory response helps to contain and eradicate the pathogen; in chronic inflammatory diseases, production of these cytokines causes tissue damage.
Functional analysis of the tight junction
Authors: Cereijido Marcelino , Shoshani Liora , Contreras Ruben G
Published: November 2023

The very names used to describe the tight junction (TJ) since it was discovered a century and a half ago reveal that, actually, it was not expected to function: ‘Schlussleisten’, ‘terminal bars’, ‘bandelettes de fermeture’, ‘hoops’, ‘occluding junctions’, ‘tight junctions’, ‘gaskets’, ‘attachment belts’, etc. (1). Our understanding of TJs has drastically changed subsequently due to a series of, now, well-known facts (2). Transepithelial electrical resistance (TER) ranges from 10 (proximal kidney tubule) to more than 10 000 0 cm–2 (urinary bladder), indicating that in the so-called ‘leaky epithelia’, such as the mucosa of the small intestine and the gall bladder, or the proximal tubule of the kidney, most permeating molecules do not cross through the cytoplasm of epithelial cells but circumvent them, and their flux is therefore controlled by the TJ (3, 4).
Types of Endings
Authors: Walsh Joseph
Published: November 2023

I begin by sharing two of my favorite stories about endings in clinical practice, both involving just one of my former clients. I once worked at a community mental health center where clients with serious mental disorders were sometimes seen for many years. Tara, only nineteen years old when we met, was one such client. She had a long history of sexual abuse by her father, and into her young adulthood she continued to passively enter into relationships with abusive men. Tara had low self-esteem and an unstable sense of identity. She was depressed, confused, and frequently suicidal. Tara had experienced dozens of short-term psychiatric hospitalizations prior to our first meeting. To her I was just one more in a series of social workers to whom she was referred after a hospitalization. She had not stayed involved with any professionals for longer than a few weeks.
The Solution-Focused and Narrative Theories
Authors: Walsh Joseph
Published: November 2023

The solution-focused and narrative therapies are the newest approaches to clinical practice presented in this book. They have some elements in common, as both derive from the broader social theory of constructivism. This is a different approach to understanding human behavior and the nature of change than we have considered thus far. I begin this chapter with an overview of social constructionism and then describe how the solution-focused and narrative interventions reflect this perspective on the self and the social world. Then consider how the end of intervention is approached from each perspective.
Family Theory
Authors: Walsh Joseph
Published: November 2023

Clinicians may choose from many practice theories to guide their work with families. Practitioners may select from the theories reviewed earlier in this book (reflective, cognitive, behavioral, and solution focused), as they are not specific to working with individuals. Still, family theories bring the concept of systems much more directly into the practitioner’s focus. Working with families (and groups) is qualitatively different than working with individuals. Assessing patterns of interaction and intervening with groups of people adds complexity to the process. Many practice theories specific to family work have been introduced into the literature since the 1950s.We will not review all of them, but in this chapter we will consider two major theories of family practice: family systems and structural family theory.These offer contrasting perspectives on family work and together help us get a sense of the range of available options. As in the earlier chapters we will review the theories and then consider what they recommend or imply about the ending process.
Group Interventions
Authors: Walsh Joseph
Published: November 2023

Group interventions represent a popular and effective type of service delivery in many clinical settings. They may be conducted for convenience (to accommodate large caseloads, for example) or as the intervention of choice for persons with a variety of needs who might benefit from an interpersonal process. In general, treatment groups are organized to meet social, emotional, or educational needs of participating members. There are no practice theories that are specific to group modalities. Any of the theories described in the previous chapters may be adapted for group use. Effective group leadership requires that the practitioner have an understanding of systems, however, because the processes of member interaction are often the most significant aspects of group effectiveness. Group interventions are fundamentally different than individual and family interventions in other ways as well. One of the most important aspects of groups is the fact that, when effective, they represent a positive community for the members. This community may be more supportive than other natural groups with which the clients are involved. This characteristic makes the process of ending groups challenging for the practitioner who hopes to preserve some of the “community spirit” within departing members.
Defining Volunteerism
Authors: Sherr Michael E
Published: November 2023

Daryl Reynolds, Estella Gomez, and Aaron Freeman are three people with completely different life stories. Each of them has experienced different life circumstances, has different interests and different strengths, and is at a different point in his or her life course. In the same way, each of them had different reasons for becoming a volunteer. For Daryl, becoming a volunteer began simply as a way of completing a class assignment. For Estella, after months of grieving and developing new supports, a chance encounter at a church, along with the encouragement of a friend, motivated her to take the initiative to become a hospice volunteer. Aaron was somewhat coerced into attending a meeting at a volunteer association.
Truth vs.-Loyalty Dilemmas
Authors: Strom-Gottfried Kim
Published: November 2023

Truth-vs.-loyalty dilemmas are a common feature of practice with minors. At their essence, the dilemmas in this category involve the conflict between the need to share information and the value of upholding implicit or explicit promises to do otherwise. All dilemmas involving the right to privacy fall into this category. Conflict-of-interest dilemmas often do as well. In practice with children and adolescents, the common standards of confidentiality are challenged by the rights and interests of parents and the social institutions that limit minors’ rights.
Sister Jean Abbott: Bringing Healing to Victims of Trauma Worldwide
Authors: Curley Jami , Tebb Susan S
Published: November 2023

The effects of war and civil conflicts on a survivor’s mind and body can be devastating, particularly when abuse and torture are involved. According to the World Health Organization (2002), depression and anxiety, suicidal tendencies, alcohol abuse, and posttraumatic stress disorder (PTSD) are among the psychological and behavioral problems resulting from the collective violence that ensues from the chaos and disorder of civil unrest. Many victims flee their homeland out of fear for their lives or are forcibly displaced to other countries in search of asylum. Known as refugees, these people often seek safety and protection from their home countries. At the end of 2006, approximately 14 million refugees and asylum seekers were in need of protection worldwide (U.S. Committee for Refugees and Immigrants, 2007). Of the 69,400 refugees that were resettled in other countries, more than 41,000 were resettled in the United States (U.S. Committee for Refugees and Immigrants, 2007).
Statistical Training for Social Workers
Authors: Fischer Joel
Published: November 2023

The increased emphasis on research methods in social work education has prompted a great deal of confusion and disagreement over the extent and type of research content to be included in curricula (Austin, 1978; Heineman, 1981; Hudson, 1982; Glisson, 1982; Karger, 1983). The debate has been particularly intensive over the extent to which social workers should be trained in statistics (Cowger, 1984; Glisson, 1985; Pieper, 1985). Currently, there is considerable disagreement about the value of statistical training and an enormous variation among social workers in their ability to either understand or undertake statistical analyses. This article has four objectives related to statistical training: 1) to establish the value of statistical training for social workers; 2) to assess current levels of training provided to social workers; 3) to present general, educational principles for statistical training in social work; and 4) to provide specific objectives and curricula for bachelor’s, master’s, and doctoral social work programs covering the continuum of statistical methodologies in the three programs.
Use of Computers in Evaluation and Practice
Authors: Fischer Joel
Published: November 2023

As the prices of personal computers continue to drop, and programs for their use become more accessible and easy to use, it is inevitable that practitioners in the human services will come to rely on personal computers to help manage and enhance their practice. Computers increasingly are becoming a crucial part of evaluation and practice. In fact, one might argue that recent advances in computer technology have revolutionized the way practitioners engage in practice and evaluation. This development has been hastened by three major phenomena: (1) the increasing sophistication of users of computers–computers are available at home and at work, and more and more people are becoming familiar with their use; (2) the incredible drop in prices of personal computers, making them more accessible to people than ever before; and (3) recognition by practitioners of the value of computers for evaluation and practice. Indeed, some practitioners feel completely hampered in their practice and evaluation activities if they are denied access to their computers for even a short time. (You can include the authors in this latter group.)
From Environmental Despair to the Ecological Self: Mindfulness and Community Action
Authors: Lysack Mishka
Published: November 2023

One evening in February of 2007, I was watching a CBC documentary report on the dramatic increase in the slaughter of African elephants for ivory. The journalist reported that in 2006 alone, 26,000 elephants—5 percent of the entire population on earth—had been ruthlessly poached, despite the presence of laws and the efforts of sanctuary officers to protect the elephants.
Porphyro’s ‘Ancient Ditty’: Text and Topology in The Eve of St Agnes/‘La Belle Dame sans Merci’
Authors: Marggraf-Turley Richard
Published: November 2023

This article explores non-orientable textualities and self-quotation in Romantic poetry, focusing on two of John Keats’s major poems: The Eve of St Agnes and ‘La Belle Dame sans Merci’. It proposes that an intricate web of intertextuality between Keats’s romance and ballad can be conceptualized in topological terms. Central to this approach is the application of the Klein bottle—a single-sided, non-orientable structure—as a model for understanding the complex ways in which the two poems are connected to themselves and each other. The analysis is extended to include the reflexive dynamics of Robert Burns’s bawdy song, ‘Nine Inch Will Please a Lady’ and Richard Roos’s Middle English translation of Alain Chartier’s ‘La Belle Dame sans Mercy’. Finally, the essay argues that Keats’s romance and ballad can be envisioned not as distinct literary works but rather as topological regions on a larger, continuous textual surface—a spatial paradigm that has the potential to provide a fresh lens for examining intertextual literature more widely.
Epidemiology and Management of Plant Viruses Under a Changing Climate
Authors: Jeger Michael J. , Fereres Alberto , Malmstrom Carolyn E. , Mauck Kerry E. , Wintermantel William M.
Published: November 2023

Plant viruses are an ever-present threat to agricultural production and provide a wide array of symptoms resulting in economic losses throughout the world. Diseases can be transmitted by insect vectors, as well as through pollen, seed, and other means. With the increased globalization of agriculture, the introduction of new viruses from exotic locations and their establishment in new production regions and even new crops is a growing concern. Advancing knowledge of the epidemiology of plant viruses including development of new diagnostic methods, virus surveillance, and modeling, virus ecology and evolution, virus interactions with insect vectors, and other factors are important toward reducing the spread of plant viruses and managing virus diseases.
Defining thein vivorole of mTORC1 in thyrocytes by studying the TSC2 conditional knockout mouse model
Authors: Rossetti Camila , Lourençoni Bruna , Peçanha Flavia , Franco Aime T , Nosé Vania , Carneiro Everardo , Lew John , Bernal-Mizrachi Ernesto , Werneck-de Castro Joao Pedro
Published: November 2023

The thyroid gland is susceptible to abnormal epithelial cell growth, often resulting in thyroid dysfunction. The serine-threonine protein kinase mechanistic target of rapamycin (mTOR) regulates cellular metabolism, proliferation, and growth through two different protein complexes, mTORC1 and mTORC2. The PI3K-Akt-mTORC1 pathway’s overactivity is well associated with heightened aggressiveness in thyroid cancer, but recent studies indicate the involvement of mTORC2 as well. To elucidate mTORC1’s role in thyrocytes, we developed a novel mouse model with mTORC1 gain of function in thyrocytes by deleting Tuberous Sclerosis Complex 2 (TSC2), an intracellular inhibitor of mTORC1. The resultingTPO-TSC2KOmice exhibited a significant reduction in TSC2 levels, leading to a six-fold increase in mTORC1 activity. Thyroid glands of both male and femaleTPO-TSC2KOmice displayed rapid enlargement and continued growth throughout life, accompanied by heterogeneity among thyroid follicles, larger follicles, increased colloid and epithelium. We observed elevated thyrocyte proliferation as indicated by Ki67 staining and elevated Cyclin D3 expression in theTPO-TSC2KOmice. mTORC1 activation resulted in a progressive downregulation of key genes involved in thyroid hormone (TH) biosynthesis, including thyroglobulin, thyroid peroxidase, and sodium-iodide symporter (NIS), while TTF1, PAX8, and MCT8 mRNA levels remained unaffected. NIS protein expression was also diminished inTPO-TSC2KOmice. Treatment with the mTORC1 inhibitor rapamycin prevented thyroid mass expansion and restored the gene expression alterations inTPO-TSC2KOmice. Although T4, T3and TSH plasma levels were normal at 2 months of age, a slight decrease in T4and an increase in TSH levels were observed at 6 and 12 months of age while T3 remained similar inTPO-TSC2KOcompared to littermate control mice.TPO-TSC2KOmice aged to 12 months or older developed aberrant thyroid conditions, including follicular hyperplasia, inflammation, and thyroid tumors. In conclusion, our thyrocyte-specific mouse model reveals that mTORC1 activation inhibits TH biosynthesis, suppresses thyrocyte gene expression, and promotes growth and proliferation. Chronic mTORC1 activation leads to thyroid tumor formation, highlighting the role of mTORC1 in thyroid dysfunction and tumorigenesis.
OVO Positively Regulates Essential Maternal Pathways by Binding Near the Transcriptional Start Sites in theDrosophilaFemale Germline
Authors: Benner Leif , Muron Savannah , Gomez Jillian G. , Oliver Brian
Published: November 2023

Differentiation of female germline stem cells into a mature oocyte includes the expression of RNAs and proteins that drive early embryonic development inDrosophila. We have little insight into what activates the expression of these maternal factors. One candidate is the zinc-finger protein OVO. OVO is required for female germline viability and has been shown to positively regulate its own expression, as well as a downstream target,ovarian tumor, by binding to the transcriptional start site (TSS). To find additional OVO targets in the female germline and further elucidate OVO’s role in oocyte development, we performed ChIP-seq to determine genome-wide OVO occupancy, as well as RNA-seq comparing hypomorphic and wild type rescueovoalleles. OVO preferentially binds in close proximity to target TSSs genome-wide, is associated with open chromatin, transcriptionally active histone marks, and OVO-dependent expression. Motif enrichment analysis on OVO ChIP peaks identified a 5′-TAACNGT-3′ OVO DNA binding motif spatially enriched near TSSs. However, the OVO DNA binding motif does not exhibit precise motif spacing relative to the TSS characteristic of RNA Polymerase II complex binding core promoter elements. Integrated genomics analysis showed that 525 genes that are bound and increase in expression downstream of OVO are known to be essential maternally expressed genes. These include genes involved in anterior/posterior/germ plasm specification (bcd, exu, swa, osk, nos, aub, pgc, gcl), egg activation (png, plu, gnu, wisp, C(3)g, mtrm), translational regulation (cup,orb,bru1, me31B), and vitelline membrane formation (fs(1)N,fs(1)M3,clos). This suggests that OVO is a master transcriptional regulator of oocyte development and is responsible for the expression of structural components of the egg as well as maternally provided RNAs that are required for early embryonic development.
A single locus determines praziquantel response inSchistosoma mansoni
Authors: Chevalier Frédéric D. , Le Clec’h Winka , Berriman Matthew , Anderson Timothy J.C.
Published: November 2023

We previously performed a genome-wide association study (GWAS) to identify the genetic basis of praziquantel (PZQ) response in schistosomes, identifying two quantitative trait loci (QTL) situated on chromosome 2 and chromosome 3. We reanalyzed this GWAS using the latest (v10) genome assembly showing that a single locus on chromosome 3, rather than two independent loci, determines drug response. These results reveal that praziquantel response is monogenic and demonstrates the importance of high-quality genomic information.
Germlinecisvariant determines epigenetic regulation of the anti-cancer drug metabolism gene dihydropyrimidine dehydrogenase (DPYD)
Authors: Zhang Ting , Ambrodji Alisa , Huang Huixing , Bouchonville Kelly J. , Etheridge Amy S. , Schmidt Remington E. , Bembenek Brianna M. , Temesgen Zoey B. , Wang Zhiquan , Innocenti Federico , Stroka Deborah , Diasio Robert B. , Largiadèr Carlo R. , Offer Steven M.
Published: November 2023

Enhancers are critical for regulating tissue-specific gene expression, and genetic variants within enhancer regions have been suggested to contribute to various cancer-related processes, including therapeutic resistance. However, the precise mechanisms remain elusive. Using a well-defined drug-gene pair, we identified an enhancer region for dihydropyrimidine dehydrogenase (DPD,DPYDgene) expression that is relevant to the metabolism of the anti-cancer drug 5-fluorouracil (5-FU). Using reporter systems, CRISPR genome edited cell models, and human liver specimens, we demonstratedin vitroandvivothat genotype status for the common germline variant (rs4294451; 27% global minor allele frequency) located within this novel enhancer controlsDPYDtranscription and alters resistance to 5-FU. The variant genotype increases recruitment of the transcription factor CEBPB to the enhancer and alters the level of direct interactions between the enhancer andDPYDpromoter. Our data provide insight into the regulatory mechanisms controlling sensitivity and resistance to 5-FU.
MetalPrognosis: a Biological Language Model-based Approach for Disease-Associated Mutations in Metal-Binding Site prediction
Authors: Jia Runchang , He Zhijie , Wang Cong , Guo Xudong , Li Fuyi
Published: November 2023

Protein-metal ion interactions play a central role in the onset of numerous diseases. When amino acid changes lead to missense mutations in metal-binding sites, the disrupted interaction with metal ions can compromise protein function, potentially causing severe human ailments. Identifying these disease-associated mutation sites within metal-binding regions is paramount for understanding protein function and fostering innovative drug development. While some computational methods aim to tackle this challenge, they often fall short in accuracy, commonly due to manual feature extraction and the absence of structural data. We introduce MetalPrognosis, an innovative, alignment-free solution that predicts disease-associated mutations within metal-binding sites of metalloproteins with heightened precision. Rather than relying on manual feature extraction, MetalPrognosis employs sliding window sequences as input, extracting deep semantic insights from pre-trained protein language models. These insights are then incorporated into a convolutional neural network, facilitating the derivation of intricate features. Comparative evaluations show MetalPrognosis outperforms leading methodologies like MCCNN and PolyPhen-2 across various metalloprotein test sets. Furthermore, an ablation study reiterates the effectiveness of our model architecture. To facilitate public use, we have made the datasets, source codes, and trained models for MetalPrognosis online available athttp://metalprognosis.unimelb-biotools.cloud.edu.au/.
The Taurus Mountains, the hotspot of Western Palearctic biodiversity, is under danger: marble quarries affect wildlife
Authors: Albayrak Tamer , Yılmaz Tamer
Published: November 2023

The Taurus Mountains in the Mediterranean Coastal Basin, considered a biodiversity hotspot, have a rich biodiversity in the Western Palearctic. The number of marble quarries in the Taurus Mountains has dramatically expanded over the past ten years. The objectives of this study are to (i) determine the impacts of quarrying on wildlife; (ii) determine the potential impacts of quarrying on the future of Taurus. A total of 57547 photos and video images were analyzed on 5447 photo-trap days in two areas, the marble quarries and the control areas. Using 97 randomly selected marble quarries, the area they cover and their annual growth rates were determined. The most commonly seen animals were the wolf, fox, lynx, and wild boar in the control area, and the jackal and hare in the marble quarries (p< 0.001). Additionally, we found a significant positive correlation between the distance of the geographical center of the marble quarries and the number of dates of Wolf, Fox and Wild Boar and a negative significant correlation for hare (p< 0.05). A positive correlation was found between the area of marble quarries and the duration of operation (R= 0.89,p< 0.00). The waste from quarries, which makes up 79.7% of the total land used for this purpose, is the greatest cause of habitat degradation. According to calculations, even if no new marble quarries are built as of right now, 7.14% of the Taurus may have disappeared by the year 2027, and by the year 2032, 8.25% of the Taurus ecosystems may have disappeared completely. The Taurus Mountains, a center of Western Palearctic biodiversity, are being threatened by the marble quarries. This study advances our knowledge of how marble quarries may affect wildlife. New strategies must be developed as soon as possible to protect the Taurus Mountains, the hotspot of the Mediterranean basin.

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We conducted a one-year photo trap study on the effects of marble quarries on wildlife in the Taurus Mountains, a significant biodiversity hotspot. Our research showed that wild animals prefer areas without marble quarries, and their density rises as they get farther from the quarry’s core. Photograph by Tamer Yılmaz
Cellular Uptake and Fate of Cationic Polymer-Coated Nanodiamonds Delivering siRNA: A Mechanistic Study
Authors: Majer Jan , Kindermann Marek , Pinkas Dominik , Chvatil David , Cigler Petr , Libusova Lenka
Published: November 2023

Gene silencing using small interfering RNAs (siRNAs) is a selective and promising approach for treatment of numerous diseases. However, broad applications of siRNAs are compromised by their low stability in a biological environment and limited ability to penetrate cells. Nanodiamonds (NDs) coated with cationic polymers can enable cellular delivery of siRNAs. Recently, we developed a new type of ND coating based on a random copolymer consisting of (2-dimethylaminoethyl) methacrylate (DMAEMA) and N-(2-hydroxypropyl) methacrylamide (HPMA) monomers. These hybrid ND-polymer particles (Cop+-FND) provide near-infrared fluorescence, form stable complexes with siRNA in serum, show low toxicity, and effectively deliver siRNA into cellsin vitroandin vivo. Here, we present data on the mechanism of cellular uptake and cell trafficking of Cop+-FND:siRNA complexes and their ability to selectively suppress mRNA levels, as well as their cytotoxicity, viability and colloidal stability. We identified clathrin-mediated endocytosis as the predominant entry mechanism for Cop+-FND:siRNA into U-2 OS human bone osteosarcoma cells, with a substantial fraction of Cop+-FND:siRNA following the lysosome pathway. Cop+-FND:siRNA potently inhibited the target GAPDH gene with negligible toxicity and sufficient colloidal stability. Based on our results, we suggest that Cop+-FND:siRNA can serve as a suitablein vivodelivery system for siRNA.
Influence of Reinforcement and Its Omission on Trial-by-Trial Changes of Response Bias in Perceptual Decision-Making
Authors: Stüttgen Maik C. , Dietl Andrea , Eckert Vanya V. Stoilova , Ferrer Luis de la Cuesta , Blanke Jan-Hendrik , Koß Christina , Jäkel Frank
Published: November 2023

Discrimination performance in perceptual choice tasks is known to reflect both sensory discriminability and non-sensory response bias. In the framework of signal detection theory (SDT), these aspects of discrimination performance are quantified through separate measures, sensitivity (d’) for sensory discriminability and decision criterion (c) for response bias. However, it is unknown how response bias (i.e., criterion) changes at the single-trial level as a consequence of reinforcement history. We subjected rats to a two-stimulus two-response conditional discrimination task with auditory stimuli and induced response bias through unequal reinforcement probabilities for the two responses. We compared three SDT-based criterion learning models in their ability to fit experimentally observed fluctuations of response bias on a trial-by-trial level. These models shift the criterion by a fixed step (1) after each reinforced response, or (2) after each non-reinforced response, or (3) after both. We find that all three models fail to capture essential aspects of the data. Prompted by the observation that steady-state criterion values conformed well to a behavioral model of signal detection based on the generalized matching law, we constructed a trial-based version of this model and find that it provides a superior account of response bias fluctuations under changing reinforcement contingencies.