bluuebunny/crossref_metadata_2025 huggingface dataset:
Genes, genomes, and chips
Authors: Schena Mark
Published: November 2023

This chapter provides an overview of the microarray or biochip field, describing biological framework, historical perspective, applications, and future trends. Microarray assays are summarized and compared to traditional approaches. Methodological underpinnings of biochips are emphasized. The information content of the genome is carried hereditarily as deoxyribonucleic acid (DNA). The size and composition of a given genomic sequence determines the form and function of the resultant organism. In general, genomic complexity is proportional to the complexity of the organism. Relatively simple organisms such as bacteria have genomes in the 1– 5 million base (megabase) range while mammalian genomes including human are approximately 3000 megabases; genomes from organisms of intermediate complexity such as worms and insects are typically 100– 200 megabases.
Antisense oligonucleotide scanning arrays
Authors: Elder John k. , Johnson Martin
Published: November 2023

Antisense oligonucleotides are short DNA sequences, typically between 15-25 nucleotides, that can bind to a complementary mRNA target by Watson-Crick base pairing and selectively inhibit the expression of the target gene from among the 80000 or so estimated to be present in a typical mammalian cell (1, 2). This, in principle, makes possible the rational design of DNA-based therapeutic drugs for specific inhibition of any gene of known sequence. Antisense oligonucleotide drugs are currently in advanced stages of clinical trials for viral diseases and cancer (3, 4). Antisense oligonucleotides are also a useful tool in biological studies of gene function. A major issue in antisense development is the selection of those reagents that work effectively. The ability to bind to the target mRNA influences the efficacy of an oligonucleotide as an antisense reagent. Oligonucleotides targeted to regions separated by only a few bases can have markedly different antisense effects (5). There is compelling evidence that the presence of secondary structure in mRNA influences the formation of intermolecular heteroduplexes between the mRNA and the antisense oligonucleotide (5, 6). Computer programs such as mfold (7), designed to predict secondary structure of RNAs, have a limited utility in the selection of antisense oligonucleotides (5, 8); empirical selection of those reagents that can form stable heteroduplexes with the target mRNA is more effective.
Applications for analysis of contractile functions in dividing and migrating tissue culture cells
Authors: Fishkind Douglas J , Romenskaia Irina , Bao Yun , Manubay Christine M
Published: November 2023

The cytoskeleton is composed of a dynamic network of filament systems that form the scaffolding and machinery responsible for spatially and temporally integrating a variety of cell functions. In addition to maintaining cell shape and polarity, cytoskeletal polymers orchestrate a variety of cell movements, including intracellular transport, chromosome segregation, cell locomotion, and cell division. Such activities result from the direct interaction of polymer systems such as actin filaments and microtubules that combine with a vast array of complementary binding proteins and molecular motors to transduce mechanochemical energy into active force production. The exquisite sensitivity and timing of such events is controlled in turn by a complex network of signalling molecules that co-operatively function to stimulate and regulate productive interactions leading to force generation and mechanical transduction (1).
Cell shape control and mechanical signalling through the cytoskeleton
Authors: Goldmann Wolfgang H , Alonso Jose Luis , Bojanowski Krzysztof , Brangwynne Clifford , Chen Christopher S , Chicurel Marina E , Dike Laura , Huang Sui , Lee Kyung-Mi , Maniotis Andrew , Mannix Robert , Mcnamee Helen , Meyer Christian J , Naruse Keiji , Parker Kevin Kit , Plopper George , Polte Thomas , Wang Ning , Yan Li , Ingber Donald E
Published: November 2023

For the past twenty years, our group has explored the possibility that cells and tissues use a form of architecture, known as ‘tensegrity’, to control their shape and to transduce mechanical signals into changes in biochemistry and gene expression (1-5). The importance of the tensegrity paradigm is that it predicts that the form and function of living cells are controlled through changes in mechanical interactions between cells and their underlying extracellular matrix (ECM) adhesions that, in turn, alter cytoskeletal and nuclear structure inside the cell (1-6).
Assessment of DNA damage in apoptosis
Authors: Yoshida Akira , Shao Rong-Guang , Pommier Yves
Published: November 2023

Apoptosis is morphologically characterized by early cell shrinkage, chromatin condensation, nuclear fragmentation, cell surface blebbing, and membrane bound apoptotic bodies (1) and these changes are described in Chapter 2. One of the most extensively studied biochemical events in apoptosis is chromatin fragmentation by endonuclease activation. DNA double-strand cleavage occurs in the linker regions between nucleosomes, and produces DNA fragments that are multiples of approximately 185 base pairs (bp) (2-4). These fragments can readily be demonstrated by agarose gel electrophoresis as DNA ladders, and this method has been widely used to detect and define apoptosis. In contrast, necrosis is accompanied by random DNA breakdown, with diffuse smear in agarose gels. The appearance of the nucleosomal DNA ladder in agarose gels is an important biochemical hallmark of apoptosis, although several investigators have observed apoptosis with no detectable intemucleosomal DNA digestion (5, 6).
Analysis of cell death by flow and laser-scanning cytometry
Authors: Darzynkiewicz Zbigniew , Bedner Elzbieta , Li Xun
Published: November 2023

Flow cytometry, by providing the possibility of rapid, accurate, and unbiased measurements of a variety of cell components on a cell by cell basis, has become an indispensable methodology in the analysis of cell death (see reviews in refs 1-6). One area of application of flow cytometry is in studies of the mechanism of cell death.
Cell-mediated cytotoxicity and cell death receptors
Authors: Naval Javier , Anel Alberto
Published: November 2023

T cell-mediated cytotoxicity in short time assays (3-4 h) is achieved through two main mechanisms. A first mechanism, Ca2+ dependent, requires the action of the pore-forming protein perforin and a subfamily of serine proteases named granzymes or fragmentins (1). The second mechanism, which is Ca2+ independent for its execution, requires the expression of Fas (Apo-1/CD95) at the target cell surface (2), and of the Fas ligand (FasL) at the effector cell surface (3).
Methods of measuring Bcl-2 family proteins and their functions
Authors: Reed John C , Xie Zhihua , Kitada Shinichi , Zapata Juan M , Xu Qunli , Schendel Sharon , Krajewska Maryla , Krajewski Stanislaw
Published: November 2023

Bcl-2 family proteins play critical roles in the regulation of programmed cell death and apoptosis (reviewed in refs 1-4). Changes in the levels or bioactivities of these proteins are associated with a variety of physiological processes where cell death occurs, including fetal development, haematopoietic and immune cell differentiation, oogenesis, mammary gland involution, and normal cell turnover in the epidermis, gut, and several other tissues. Moreover, pathological alterations in the expression of Bcl-2 family proteins have been documented in cancer, autoimmunity, immunodeficiency, heart failure, stroke, and other diseases (reviewed in refs 5-9). Consequently, methods for assessing the relative levels and bioactivities of Bcl-2 family proteins can be of interest to scientists in a board range of disciplines.
Scaling-up of animal cell cultures
Authors: Griffiths Bryan
Published: November 2023

Small scale culture of cells in flasks of up to 1 litre volume (175 cm2 surface area) is the best means of establishing new cell lines in culture, for studying cell morphology and for comparing the effects of agents on growth and metabolism. However, there are many applications in which large numbers of cells are required, for example extraction of a cellular constituent (109 cells can provide 7 mg DNA); to produce viruses for vaccine production (typically 5 X 1010 cells per batch) or other cell products (interferon, plasminogen activator, interleukins, hormones, enzymes, erythropoietin, and antibodies); and to produce inocula for even larger cultures. Animal cell culture is a widely used production process in biotechnology, with systems in operation at scales over 10 000 litres. This has been achieved by graduating from multiples of small cultures, an approach which is tedious, labour-intensive, and expensive, to the use of large ‘unit process’ systems. Although unit processes are more cost-effective and efficient, achieving the necessary scale-up has required a series of modifications to overcome limiting factors such as oxygen limitation, shear damage, and metabolite toxicity. One of the aims of this chapter is to describe these limitations, indicate at what scale they are likely to occur, and suggest possible solutions. This theme has to be applied to cells that grow in suspension and also to those that will only grow when attached to a substrate (anchorage-dependent cells). Another aspect of scale-up that will be discussed is increasing unit cell density 50- to 100-fold by the use of cell immobilization and perfusion techniques.
Development of serum-free media
Authors: Karmiol Severin
Published: November 2023

The removal of serum or other undefined components from cell culture medium involves a multifaceted approach. This is mainly due to the interactive nature of cell culture systems. Cell culture systems require various components: basal nutrients, a set of supplements that convey information, such as growth factors, mitogens, hormones, and cytokines, and for anchorage-dependent cells, a substrate. In designing any cell culture system attention must be paid to all these components and their interactions.
Tissue engineering
Authors: Brown Robert A , Porter Rebecca A
Published: November 2023

Tissue engineering (TE) is the application of engineering principles to cell culture for the purpose of constructing functional anatomical units, normally for reconstructive surgery. There are three main components: cell biology, materials science (polymer/protein biochemistry), and biological engineering.
Senescence, apoptosis and necrosis
Authors: Kill Ian R , Faraghert† Richard G A
Published: November 2023

Populations of cells which will divide forever in culture (continuous cell lines) differ from those which cease to expand after several weeks or months of growth (finite cell lines). The end of the proliferative lifespan of a cell culture has been loosely termed as either its ‘senescence’ or its ‘death’. These states are distinct biochemical entities and the causes of any failure to thrive in a cell population may involve both processes. TI1e purpose of this chapter is to describe methods for studying senescence, apoptosis, and necrosis.
Morphogenesis of skin epithelia
Authors: Coulombe Pierre A , McGowan Kevin
Published: November 2023

By virtue of its strategic location at the surface of the body, the skin has multiple functions that define in many ways the relationship that the whole organism has with its external environment (1−4). The epithelial compartment of the skin acts as a barrier that restricts the exchange of water-soluble compounds, prevents the entry of infectious micro-organisms, filters out harmful ultraviolet irradiation, and contributes to immunological surveillance. In addition, epithelial specializations such as the hair and nail contribute significantly to thermal insulation, tactile sensation, sexual behaviours, and, in some cases, flight (feathers) and natural defence (claws). These various epithelial compartments lie over, or in some cases are embedded within, a connective tissue known as the dermis. Through its rich vascularization and innervation and a complex extracellular matrix, the dermis makes essential contributions to the properties and functions of skin. The regulation of cutaneous blood flow represents an important homeostatic mechanism for the regulation of body heat, and the afferent and efferent innervation of the skin are an integral part of sensory perception (3, 4). More relevant to this text, however, the dermis is the source of instructions that play essential roles in the morphogenesis and the homeostasis of mature skin tissue (5−13).
Kinetic modeling for biosensors
Authors: Bartlett Philip N , Toh Chee-Seng
Published: November 2023

The purpose of a kinetic model of a biosensor is to identify the key experimental factors (such as the rates of reactions, rates of mass transport, loading of the bio-recognition component, etc.), which determine the response, or output, of the sensor and to then provide a link between these key experimental factors and the concentration of the analyte and the sensor response. Thus, modeling provides a mathematical description of the physical processes occurring within the system. By applying kinetic modeling to enzyme electrodes and biosensors, we can derive a number of advantages. It is clear that several different kinetic processes are involved in the overall functioning of any enzyme electrode or biosensor.
Specific cell types and their requirements
Authors: Sato J Denry , Barnes David W
Published: November 2023

Although attempts at maintaining tissue explants in vitro have been reported since 1907, the beginning of the modern era of cell culture was marked by the establishment of the first cell lines, the mouse L-cell fibroblast line and the human HeLa cervical adenocarcinoma line, and by initial studies to determine the nutritional requirements of cells in culture (1–3). However, it was not until the 1960s that functional differentiated mammalian cell lines were first established from transplantable tumours (4, 5) following the realization that measures had to be taken to prevent the routine overgrowth of differentiated cells by fibroblasts in culture (6). A wide range of normal, immortalized, and transformed cell types can now be maintained or propagated in vitro (7–13). In general, normal cells, which may divide slowly or intermittently in vivo, exhibit a reduced capacity to proliferate in vitro in comparison with their partially or fully transformed counterparts. Furthermore, cells that cease dividing in vivo after undergoing terminal differentiation, such as neurons, skeletal muscle cells, and adipocytes, do not proliferate in vitro. However, as the growth requirements of individual cell types become more explicitly defined and as the interactions between cells and their environments are better understood, cells are able to survive longer or proliferate to a greater extent in culture. Although cells in culture, particularly continuous cell lines, may not display all the properties of differentiated cells in vivo, strides are being made towards the goal of being able to investigate physiologically relevant properties of specialized cells in completely defined culture environments.
Finding Volunteers for Partnerships
Authors: Sherr Michael E
Published: November 2023

Social work practice with volunteers begins with a simple need social workers must find volunteers to develop partnerships. But finding volunteers is a process that takes time and effort. It requires the application of basic helping skills, such as building rapport; reflective listening; and expressing warmth, genuineness, and appreciation for others. Just as social workers learn to be conscious and deliberate in how they develop and maintain trusting relationships in clinical practice, they must do the same in strategically developing a diverse network of genuine relationships with people who may become volunteer partners. This chapter will assist social workers in developing a strategic network of genuine relationships that can lead to fruitful volunteer partnerships.
Understanding Ethics
Authors: Strom-Gottfried Kim
Published: November 2023

On January 2, 2002, the last day of his school’s winter break, twelve year old J. Daniel Scruggs hanged himself with a necktie in the bedroom closet of the small apartment he shared with his mother and nineteen-year-old sister. Six days earlier, the Department of Children and Families had dismissed allegations of neglect against Daniel’s mother due to a lack of evidence.
Ethical and Clinical Decision Making
Authors: Strom-Gottfried Kim
Published: November 2023

When asked what process they use for resolving dilemmas, professionals often respond,”I trust my gut.” Sometimes gut-level decisions are the result of an internalized, almost automatic ethical decision-making strategy honed over years of use until it develops into a reflexive response to addressing dilemmas (Gladwell, 2005). In other cases, though, intuition is a fly-by-the-seat-of-your-pants enterprise, where decisions are independent, inconsistent, ungrounded, and unexamined (Gambrill, 1997). This is a hazardous approach, as it raises questions about the quality of the decisions that result and the efficacy of the social worker who reacts without forethought or consultation.
Individual-vs.-Community Dilemmas
Authors: Strom-Gottfried Kim
Published: November 2023

Individual-vs.-community dilemmas are in essence conflict-of-interest problems. These dilemmas pit the well-being of one person against that of a collective (a family, class, or community, for example). This category can also include situations in which the decision maker is torn between one person’s needs and interests and those of another individual. As such, it can also involve dilemmas in which the decision maker’s own interests are part of the equation.
Hard Truths
Authors: Strom-Gottfried Kim
Published: November 2023

In 2006, the parents and doctors of Ashley X, a six-year-old with profound brain damage, sought permission to use surgical and medical procedures to permanently stunt her growth. Once the consent of medical specialists and the hospital ethics committee was obtained, physicians performed a hysterectomy, surgically removed Ashley’s breast buds, and administered high doses of estrogen to attenuate her development (Gunther & Diekema, 2006).
The Honorable Barbara Mikulski: Fighting for Social Justice in the U.S. Senate
Authors: Collins Kathryn , Lazzari Marceline
Published: November 2023

Barbara Ann Mikulski was raised in an extended family in a close-knit, Polish-Catholic, working-class neighborhood in East Baltimore. Her early experiences in these environs, combined with sixteen years of Catholic education, were instrumental in shaping the philosophy that has guided her life. Recalling those years, she has said, ‘‘The neighborhood was really our extended family. If Bethlehem Steel was on strike, my father extended credit to the guys. In the middle of a snowstorm, if he didn’t see Miss Sophie, who was a diabetic, he called down there to see if she needed anything. I ran down the oranges’’ (Broder, 1980, p. 149). This was a living lesson in the moral obligations we each have to look out for our neighbors, a lesson Mikulski took very seriously.
Katherine A. Kendall :The Founder of International Social Work
Authors: Watkins Julia
Published: November 2023

It is fair to say that international social work would not be what it is, or where it is today, without Katherine Kendall’s tireless efforts to expand its reach. Born in Scotland during the Progressive Era (and the halcyon days of Hull House!) and undoubtedly influenced by limitations society placed on her as a woman, Katherine fit well in a profession whose core principles include self-determination and the according of respect and dignity to all. An example of Katherine’s worldwide influence on social work is found in the fact that two other women in this book—Armaity Desai and Sattareh Farman Farmaian—cite her as a most valuable source of consultation and support in attaining their professional goals in their respective countries.
Sattareh Farman Farmaian: Bringing Social Work Education to Iran
Authors: Lieberman Alice
Published: November 2023

Born into the ruling Qajar dynasty in Iran, Sattareh Farman Farmaian brought social work to her country when she founded the Tehran School of Social Work. At the time, the concept of professional social work was so foreign to this tribal culture that there was no equivalent in the Persian language for ‘‘social worker,’’ so she made one up: madadkar, which means ‘‘one who helps.’’ But that, she says, is not the most important professional contribution she made in her life. I visited her in October 2006, at her home in Los Angeles. It is filled with photos, books, and art that reflect her devotion to family, and her love for this rich culture.
New and Emerging Methods of Direct Practice: The Revolution in Social Work
Authors: Fischer Joel
Published: November 2023

Social work is in the midst of a revolution. As revolutions go, it is a rather quiet revolution, but it is a revolution nevertheless. It is a revolution in the ways social workers are beginning to view knowledge and practice and in the ways social workers are beginning to use knowledge and conduct practice. It is a revolution that portends great improvements in the direct-practice branch of social work and one that bodes well for dramatically increasing the success of the profession in helping others.
A Framework for Evaluating Empirical Research Reports
Authors: Fischer Joel
Published: November 2023

Empirical research reports are defined in this chapter as published articles based on studies designed to contribute to the social work knowledge base through rigorous, replicable means. A methodology for evaluating the significance and validity of the knowledge derived from such reports is suggested in a framework whose value rests on answers to two basic questions: The first question is addressed in the theme of this book: Research and evaluation should be applicable in social work practice situations, and the field of social work should not be dichotomized into practice and research orientations. These concepts are based on the belief that systematic, orderly procedures of empirical social work research and evaluation provide the most productive means to organize, understand, test, and develop social work knowledge. The capacity to perform competently in the social work profession, therefore, is based on the ability to analyze and utilize the results of social work research and evaluation.
An Eclectic Approach for Persons with Substance-related Disorders
Authors: Fischer Joel
Published: November 2023

There is little question that substance abuse is one of the hot topics from the 1980s up until today. Both the lay and the professional literature are rife with references to the problems and dangers associated with substance use and abuse—and rightly so. The direct and indirect costs of substance abuse—in terms of dollars and lives—are enormous. However, the real issues involved sometimes are lost in the virtual national hysteria that has arisen since the days of the Reagan administration. The hysteria regarding drug usage in the United States has been well documented by Abbie Hoffman (1987) in his book Steal This Urine Test. Hysteria also can be seen, perhaps, in the statement of a graduate social work student who announced in class that an alcoholism expert in a lecture had asserted that 80 percent of human service professionals either have problems with alcohol themselves or come from families where at least one member does. Finally, the national preoccupation with substance abuse can be seen in President Bush’s declaration in September of 1989 that “the gravest domestic threat facing our nation today is drugs” (Honolulu Advertiser, September 6, 1989, p. A-4).
Evidence-Based Practice
Authors: Fischer Joel
Published: November 2023

Evidence-based practice (EBP) is one of the most important developments in decades for the helping professions—including medicine, nursing, social work, psychology, public health, counseling, and all the other health and human service professions (Briggs & Rzepnicki, 2004; Brownson et al., 2002; Dawes et al., 1999; Dobson & Craig, 1998a, 1998b; Gilgun, 2005; Roberts & Yeager, 2004; Sackett et al., 2000). That is because evidence-based practice holds out the hope for practitioners that we can be at least as successful in helping our clients as the current available information on helping allows us to be. Both the importance and the multidisciplinary nature of EBP can be seen in the Roberts and Yeager (2004) compendium, Evidence-Based Practice Manual, a collection of chapters describing the meaning, methods, and examples of EBP. Evidence-based practice represents both an ideology and a method. The ideology springs from the ethical principle that clients deserve to be provided with the most effective interventions possible. The method of EBP is the way we go about finding and then implementing those interventions (see, e.g., manuals on EBP methods by Gibbs, 2003; Cournoyer, 2003; and Rubin, 2007; see also http:// www.evidence.brookscole.com/index.html). Evidence-based practice represents the practitioner’s commitment to use all means possible to locate the best (most effective) evidence for any given problem at all points of planning and contacts with clients. This pursuit of the best knowledge includes extensive computer searches, as described in the following (Gibbs & Gambrill, 2002).
Mindfulness and Reflexivity: The No-Self as Reflexive Practitioner
Authors: Bères Laura G
Published: November 2023

As described in chapter 1, there is a range of different ways of consider- ing mindfulness and incorporating it into social work practice. This chapter defines mindfulness as the practice of intentionally focusing attention on what is occurring in the present moment in a nonjudgmental manner, with an interest in being rather than doing (Kabat- Zinn, 1990).
Dissection and reconstruction of the colorectal cancer tumor microenvironment
Authors: Broguiere Nicolas , Lorenzo Martin Luis Francisco , Ragusa Simone , Rivest François , Brandenberg Nathalie , Hoehnel-Ka Sylke , Dutta Devanjali , Gueye Marième , Alpern Daniel , Deplancke Bart , Kandalaft Lana , Coukos George , Homicsko Krisztian , Lutolf Matthias P.
Published: November 2023

Patient-derived organoids (PDOs) are the referencein vitrohuman disease models. However, the utility of colorectal cancer (CRC) PDOs is hindered by the lack of a tumor microenvironment (TME). To address this limitation, we built a living biobank of CRC PDOs with autologous stromal and immune TME. We characterized the original tumors and traditional monocultures using single-cell RNA-seq (scRNA-seq) and whole exome sequencing (WES) to obtain insights into cell type selection and phenotypic drift in culture. Subsequently, we developed culture conditions supporting all cell types to recapitulate the CRC-TME around PDOs. From the transcriptomes of >180k cells obtained from 260 such co-cultures, we illuminated the mutual influence of cells within CRC tumors. Based on original tumor data, atlases of predicted interactions and transcriptional networks elucidated why monocultures were altered and suggested that TME reconstruction more accurately reflected original tumor behavior. We found that inflammatory signals were absentin vitroand recovered upon co-culture with tumor-infiltrating lymphocytes (TILs). We also functionally confirmed that stromal, not cancer cells, mediated immune evasion. Additionally, stroma induced an invasive phenotype in cancer cells. From this deep dive into CRC-TME interactions, we built the human CRC-TME atlas (https://crc-tme.com/), an online portal for interactive exploration of gene expression data, prediction of cell-cell interactions at the pathway and receptor/ligand levels, transcriptional networks, and more. We anticipate PDO cultures with reconstructed TMEs will be valuable for discovery efforts, preclinical studies, and personalized medicine, with the atlas as a framework and inspiration for future CRC-TME studies.
Predicting gender from structural and functional connectomes via brain and population graph neural networks
Authors: He Yinan , Chan Yi Hao , Rajapakse Jagath C.
Published: November 2023

Gender differences in terms of structural and functional organization of the human brain have been extensively studied, but existing works have mostly been limited to single modalities. In this paper, we propose a graph attention network architecture (BrainGAT) that uses informative subjectlevel features extracted from multimodal brain graphs to construct a population graph for gender classification. We show that while the extracted subject-level features can be directly used for classification, using these graph embeddings to construct a population graph further improves model performance. On the gender classification task, BrainGAT outperforms baseline models and existing multimodal modeling approaches, achieving an accuracy of 83.13% on the Human Connectome Project dataset. Salient connections highlighted by BrainGAT include connections between the inferior parietal and dorsolateral prefrontal areas of the cortex for females, while connections within the posterior cingulate cortex are highly salient for males. In sum, BrainGAT enables multimodal data to be modelled via population graphs in a parameter-efficient way.

Clinical Relevance

Several neurological conditions exhibit significant differences across genders and multimodal studies on these diseases are increasingly prevalent. This work highlights gender differences of multimodal connectomes in neurotypical settings. These insights could help to separate multimodal disease biomarkers from fundamental gender differences.
Molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: November 2023

Introduction

High-grade serous carcinoma (HGSC) gene expression subtypes are associated with differential survival. We characterized HGSC gene expression in Black individuals and considered whether gene expression differences by race may contribute to poorer HGSC survival among Black versus non-Hispanic White individuals.

Methods

We included newly generated RNA-Seq data from Black and White individuals, and array-based genotyping data from four existing studies of White and Japanese individuals. We assigned subtypes using K-means clustering. Cluster- and dataset-specific gene expression patterns were summarized by moderated t-scores. We compared cluster-specific gene expression patterns across datasets by calculating the correlation between the summarized vectors of moderated t-scores. Following mapping to The Cancer Genome Atlas (TCGA)-derived HGSC subtypes, we used Cox proportional hazards models to estimate subtype-specific survival by dataset.

Results

Cluster-specific gene expression was similar across gene expression platforms. Comparing the Black study population to the White and Japanese study populations, the immunoreactive subtype was more common (39% versus 23%-28%) and the differentiated subtype less common (7% versus 22%-31%). Patterns of subtype-specific survival were similar between the Black and White populations with RNA-Seq data; compared to mesenchymal cases, the risk of death was similar for proliferative and differentiated cases and suggestively lower for immunoreactive cases (Black population HR=0.79 [0.55, 1.13], White population HR=0.86 [0.62, 1.19]).

Conclusions

A single, platform-agnostic pipeline can be used to assign HGSC gene expression subtypes. While the observed prevalence of HGSC subtypes varied by race, subtype-specific survival was similar.

Statement of Significance

A single pipeline was used to subtype ovarian high-grade serous carcinoma (HGSC) with array-based or RNA-Seq gene expression data. Subtype distributions differed by race, but subtype-specific survival was similar across racial groups.
Dehydrozaluzanin C- derivative protects septic mice by alleviating over-activated inflammatory response and promoting the phagocytosis of macrophages
Authors: Zou Ying-xiang , Xiang Tian-nan , Xu Li-rong , Zhang Huan , Ma Yu-he , Zhang Lu , Zhou Chun-xian , Wu Xiao , Huang Qi-lin , Lei Biao , Mu Jing-wen , Qin Xiang-yang , Jiang Xin , Zheng Yue-juan
Published: November 2023

Host-directed therapy (HDT) is a new adjuvant strategy that interfere with host cell factors that are required by a pathogen for replication or persistence. In this study, we assessed the effect of dehydrozaluzanin C-derivative (DHZD), a modified compound from dehydrozaluzanin C (DHZC), as a potential HDT agent for severe infection. LPS-induced septic mouse model and Carbapenem resistantKlebsiella pneumoniae(CRKP) infection mouse model was used for testingin vivo. RAW264.7 cells, mouse primary macrophages, and DCs were used forin vitroexperiments. Dexamethasone (DXM) was used as a positive control agent. DHZD ameliorated tissue damage (lung, kidney, and liver) and excessive inflammatory response induced by LPS or CRKP infection in mice. Also, DHZD improved the hypothermic symptoms of acute peritonitis induced by CRKP, inhibited heat-killed CRKP (HK-CRKP)-induced inflammatory response in macrophages, and upregulated the proportions of phagocytic cell types in lungs.In vitrodata suggested that DHZD decreases LPS-stimulated expression of IL-6, TNF-α and MCP-1 via PI3K/Akt/p70S6K signaling pathway in macrophages. Interestingly, the combined treatment group of DXM and DHZD had a higher survival rate and lower level of IL-6 than those of the DXM-treated group; the combination of DHZD and DXM played a synergistic role in decreasing IL-6 secretion in sera. Moreover, the phagocytic receptor CD36 was increased by DHZD in macrophages, which was accompanied by increased bacterial phagocytosis in a clathrin- and actin-dependent manner. This data suggests that DHZD may be a potential drug candidate for treating bacterial infections.
Reconciling the spectrum of RORγt+antigen-presenting cells
Authors: Park Tyler , Leslie Christina , Rudensky Alexander Y. , Brown Chrysothemis C.
Published: November 2023

Three recent contemporaneously published papers1–3showed that antigen-presenting cells (APC) expressing the nuclear receptor RORγt instruct peripheral regulatory T (pTreg) cell differentiation and establish tolerance to the gut microbiota. These studies identified a spectrum of RORγt+APCs, distinct from dendritic cells, that included type 3 innate lymphoid cells (ILC3s) as well as novel APC types. Given the discordant conclusions as to the nature of the pTreg-inducing APC and the divergent nomenclature used in these three studies, there is a clear need to reconcile these analyses and the identity of the cell types described. Our reanalysis of the single cell RNA-seq data from these studies revealed the presence of four distinct subsets of non-ILC3 RORγt+APCs, present in all three datasets reported, and confirmed expression of Itgb8, the critical factor for RORγt+APC mediated pTreg induction, in cells synonymous with the non-Aire expressing Thetis cell subset, TC IV.
A Generalized Supervised Contrastive Learning Framework for Integrative Multi-omics Prediction Models
Authors: Yang Sen , Wang Shidan , Wang Yiqing , Rong Ruichen , Li Bo , Koh Andrew Y. , Xiao Guanghua , Liu Dajiang , Zhan Xiaowei
Published: November 2023

Recent technological advances have highlighted the significant impact of the human microbiome and metabolites on physiological conditions. Integrating microbiome and metabolite data has shown promise in predictive capabilities. We developed a new supervised contrastive learning framework, MB-SupCon-cont, that (1) proposes a general contrastive learning framework for continuous outcomes and (2) improves prediction accuracy over models using single omics data. Simulation studies confirmed the improved performance of MB-SupCon-cont, and applied scenarios in type 2 diabetes and high-fat diet studies also showed improved prediction performance. Overall, MB-SupCon-cont is a versatile research tool for multi-omics prediction models.
Hippocampal Dipeptidyl Peptidase 9 Bidirectionally Regulates Memory Via Synaptic Plasticity
Authors: Zhao Ya-Bo , Wang Shi-Zhe , Guo Wen-Ting , Wang Le , Tang Xun , Li Jin-Nan , Xu Lin , Zhou Qi-Xin
Published: November 2023

It has been reported that peripherally expressed subtypes of the dipeptidyl peptidase (DPP) family, such as DPP4, modulate memory. However, interestingly whether DPP9 which one of the central nervous systems (CNS) enriched isoforms, regulates memory has not been elucidated yet. Here, we report that DPP9, which is found almost exclusively in neurons, is highly expressed and has high enzyme activity in many brain regions, especially in the hippocampus. Hippocampal DPP9 expression increases after fear memory formation. Fear memory was weakened by DPP9 knockdown and enhanced by DPP9 protein overexpression in the hippocampus. According to subsequent hippocampal proteomics, multiple pathways were enriched by DPP9 expression changes, including the peptidase pathway, which can be bidirectionally regulated by DPP9, and pathways involved in the regulation of synaptic plasticity. DPP9 interacts with its enzymatic substrate neuropeptide Y (NPY) in neurons directly. Hippocampal long-term potentiation (LTP), a form of synaptic plasticity, further confirmed the key role of DPP9 in decreasing LTP through DPP9 knockdown and enhancing LTP through its overexpression. Moreover, inhibiting DPP9 enzyme activity impairs both plasticity and memory. Besides, Affinity purification mass spectrometry (AP-MS) revealed that DPP9-interacting proteins are involved in the functions of dendritic spines and axons. By combining AP-MS and proteomics, DPP9 was shown to play a role in regulating actin functions. Taken together, our findings reveal that DPP9 affects the CNS not only through enzymatic activity but also through protein‒protein interactions. This study provides new insights into the molecular mechanisms of memory and DPP family functions.
Microbial abundance and diversity in 64-74 Ma subseafloor igneous basement from the Louisville Seamount Chain
Authors: Sylvan Jason B. , Tully Benjamin J. , Morono Yuki , Alt Jeffrey C , Grim Sharon L. , Inagaki Fumio , Koppers Anthony A.P. , Edwards Katrina J.
Published: November 2023

The aquifer in subseafloor igneous basement is a massive, continuous microbial substrate, yet sparingly little is known about life in this habitat. The work to date has focused largely on describing microbial diversity in young basement (<10 Ma) at oceanic spreading regions and ridge flanks, where the basaltic crust is still porous and fluid flow through it is active. While the prevailing belief used to be that fluid flow through older parts of the seafloor was non-existent, recent heat flow models predict that fluid moves through subseafloor basement >65 Ma, and that seamounts can act as mid-plate conduits for fluids into and out of the subsurface aquifer in older crustal settings. Here we test the hypothesis that microbial life exists in subseafloor basement >65Ma using samples collected from the Louisville Seamount Chain via seafloor drilling. Cell biomass was heterogeneous in nature and ranged from below detection to ∼104cells cm-3. Bacterial 16S rRNA genes from core samples and enrichment incubations are dominated by lineages putatively carrying out hydrocarbon oxidation and nitrogen, sulfur and metal redox processes. Samples from two different seamounts were statistically different, indicating some degree of biogeography. Archaea were not detected via quantitative polymerase chain reaction, indicating they are rare in the Louisville subsurface. Taken together, the data indicate that microbial life is indeed present in subseafloor igneous basement >65 Ma, which significantly expands the range of the subseafloor biosphere where microbial life is known to exist.

Impact Statement

The aquifer in subseafloor igneous basement is the largest continuous microbial substrate on Earth, but it is difficult to access and therefore understudied. We here collected samples from the Louisville Seamount Chain using seafloor drilling to determine if microbial life exists in the >65 Ma subseafloor basement made at these seamounts. A low biomass environment dominated by Bacteria potentially capable of using the Fe and S inherent in subseafloor basalt was detected, including Bacteria that were revived in enrichment experiments. This discovery expands the range of seafloor where confirmed microbial life exists and indicates the interior of seamounts is habitable.
Chemical inhibition of stomatal differentiation by perturbation of the master-regulatory bHLH heterodimer via an ACT-Like domain
Authors: Nakagawa Ayami , Sepuru Krishna Mohan , Yip Shu Jan , Seo Hyemin , Coffin Calvin M. , Hashimoto Kota , Li Zixuan , Segawa Yasutomo , Iwasaki Rie , Kato Hiroe , Kurihara Daisuke , Aihara Yusuke , Kim Stephanie , Kinoshita Toshinori , Itami Kenichiro , Han Soon-Ki , Murakami Kei , Torii Keiko U.
Published: November 2023

Selective perturbation of protein interactions with chemical compounds enables dissection and control of developmental processes. Differentiation of stomata, cellular valves vital for plant growth and survival, is specified by the basic-helix-loop-helix (bHLH) heterodimers. Harnessing a new amination reaction, we here report a synthesis, derivatization, target identification, and mode of action of an atypical doubly-sulfonylated imidazolone, Stomidazolone, which triggers stomatal stem cell arrest. Our forward chemical genetics followed by biophysical analyses elucidated that Stomidazolone directly binds to the C-terminal ACT-Like (ACTL) domain of MUTE, a master regulator of stomatal differentiation, and perturbs its heterodimerization with a partner bHLH, SCREAMin vitroand in plant cells. On the other hand, Stomidazolone analogs that are biologically inactive did not bind to MUTE or disrupt the SCREAM-MUTE heterodimers. Guided by structural docking modeling, we rationally designed MUTE with reduced Stomidazolone binding. These engineered MUTE proteins are fully functional and confer Stomidazolone resistancein vivo. Our study identifies doubly-sulfonylated imidazolone as a direct inhibitor of the stomatal master regulator, further expanding the chemical space for perturbing bHLH-ACTL proteins to manipulate plant development.
Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state
Authors: Brown J. Lesley , Zhang Liangliang , Rocha Pedro P , Kassis Judith A. , Sun Ming-an
Published: November 2023

Polycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that tri- methylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. Here we address the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. Our data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG- binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as “promoter-tethering elements” mediating interactions between promoter proximal PREs and distant enhancers.
Hierarchical and scaffolded phosphorylation of two degrons controls PER2 stability
Authors: Francisco Joel C. , Virshup David M
Published: November 2023

The duration of the transcription-repression cycles that give rise to mammalian circadian rhythms is largely determined by the stability of the PERIOD protein, the rate-limiting components of the molecular clock. The degradation of PERs is tightly regulated by multisite phosphorylation by Casein Kinase 1 (CK1δ/ε). In this phosphoswitch, phosphorylation of a PER2 degron (Degron 2, D2) causes degradation, while phosphorylation of the PER2 Familial Advanced Sleep Phase (FASP) domain blocks CK1 activity on the degron, stabilizing PER2. However, this model and many other studies of PER2 degradation do not include the second degron of PER2 that is conserved in PER1, termed Degron 1, D1. We examined how these two degrons contribute to PER2 stability, affect the balance of the phosphoswitch, and how they are differentiated by CK1. Using PER2-luciferase fusions and real-time luminometry, we investigated the contribution of both D2 and of CK1-PER2 binding. We find that D1, like D2, is a substrate of CK1 but that D1 plays only a ‘backup’ role in PER2 degradation. Notably, CK1 bound to a PER1:PER2 dimer protein can phosphorylate PER1 D1 in trans. This scaffolded phosphorylation provides additional levels of control to PER stability and circadian rhythms.
The role of the AP-1 adaptor complex in outgoing and incoming membrane traffic
Authors: Robinson Margaret S. , Antrobus Robin , Sanger Anneri , Davies Alexandra K. , Gershlick David C.
Published: November 2023

The AP-1 adaptor complex is found in all eukaryotes, but it has been implicated in different pathways in different organisms. To look directly at AP-1 function, we generated stably transduced HeLa cells co-expressing tagged AP-1 and various tagged membrane proteins. Live cell imaging showed that AP-1 is recruited onto tubular carriers trafficking from the Golgi apparatus to the plasma membrane, as well as onto transferrin-containing early/recycling endosomes. Analysis of single AP-1 vesicles showed that they are a heterogeneous population, which start to sequester cargo by 30 minutes after exit from the ER. Vesicle capture showed that AP-1 vesicles contain transmembrane proteins found at the TGN and early/recycling endosomes, as well as lysosomal hydrolases, but very little of the anterograde adaptor GGA2. Together, our results support a model in which AP-1 retrieves proteins from post-Golgi compartments back to the TGN, analogous to COPI’s role in the early secretory pathway. We propose that this is the function of AP-1 in all eukaryotes.

Robinson et al. investigate AP-1 function using complementary approaches on cells co-expressing tagged AP-1 and cargo proteins. Their results support a model in which AP-1 is recruited onto post-Golgi carriers and early/recycling endosomes, where it retrieves selected proteins back to the TGN.