bluuebunny/crossref_metadata_2025 huggingface dataset:
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo
Authors: Bedwell Gregory J , Jang Sooin , Li Wen , Singh Parmit K , Engelman Alan N
Published: June 2021

HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significantly reduced recurrent HIV-1 integration in vitro, LEDGF/p75 primarily occupied non-speckle-associated regions of chromatin, suggesting a previously unappreciated dynamic aspect of LEDGF/p75 functionality in HIV-1 integration targeting. Finally, we identified only six genes from patient samples—BACH2, STAT5B, MKL1, MKL2, IL2RB and MDC1—that displayed enriched integration targeting frequencies and harbored proviruses that likely contributed to cell survival. Thus, despite the known preference of HIV-1 to target cancer-related genes for integration, we conclude that genic proviruses play a limited role to directly affect cell proliferation in vivo.
DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium
Authors: Mehershahi Kurosh S , Chen Swaine L
Published: June 2021

DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
Strand-specific effect of Rad26 and TFIIS in rescuing transcriptional arrest by CAG trinucleotide repeat slip-outs
Authors: Xu Jun , Chong Jenny , Wang Dong
Published: June 2021

Transcription induced CAG repeat instability is associated with fatal neurological disorders. Genetic approaches found transcription-coupled nucleotide excision repair (TC-NER) factor CSB protein and TFIIS play critical roles in modulating the repeat stability. Here, we took advantage of an in vitro reconstituted yeast transcription system to investigate the underlying mechanism of RNA polymerase II (Pol II) transcriptional pausing/stalling by CAG slip-out structures and the functions of TFIIS and Rad26, the yeast ortholog of CSB, in modulating transcriptional arrest. We identified length-dependent and strand-specific mechanisms that account for CAG slip-out induced transcriptional arrest. We found substantial R-loop formation for the distal transcriptional pausing induced by template strand (TS) slip-out, but not non-template strand (NTS) slip-out. In contrast, Pol II backtracking was observed at the proximal transcriptional pausing sites induced by both NTS and TS slip-out blockage. Strikingly, we revealed that Rad26 and TFIIS can stimulate bypass of NTS CAG slip-out, but not TS slip-out induced distal pausing. Our biochemical results provide new insights into understanding the mechanism of CAG slip-out induced transcriptional pausing and functions of transcription factors in modulating transcription-coupled CAG repeat instability, which may pave the way for developing potential strategies for the treatment of repeat sequence associated human diseases.
Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress
Authors: Coronel Luis , Riege Konstantin , Schwab Katjana , Förste Silke , Häckes David , Semerau Lena , Bernhart Stephan H , Siebert Reiner , Hoffmann Steve , Fischer Martin
Published: June 2021

Despite its prominence, the mechanisms through which the tumor suppressor p53 regulates most genes remain unclear. Recently, the regulatory factor X 7 (RFX7) emerged as a suppressor of lymphoid neoplasms, but its regulation and target genes mediating tumor suppression remain unknown. Here, we identify a novel p53-RFX7 signaling axis. Integrative analysis of the RFX7 DNA binding landscape and the RFX7-regulated transcriptome in three distinct cell systems reveals that RFX7 directly controls multiple established tumor suppressors, including PDCD4, PIK3IP1, MXD4, and PNRC1, across cell types and is the missing link for their activation in response to p53 and stress. RFX7 target gene expression correlates with cell differentiation and better prognosis in numerous cancer types. Interestingly, we find that RFX7 sensitizes cells to Doxorubicin by promoting apoptosis. Together, our work establishes RFX7’s role as a ubiquitous regulator of cell growth and fate determination and a key node in the p53 transcriptional program.
Appetite stimulants for patients with cancer: current evidence for clinical practice
Authors: Turcott Jenny G , Zatarain-Barrón Zyanya Lucia , Cárdenas Fernández Daniela , Castañares Bolaños Diana Tamara , Arrieta Oscar
Published: June 2021

The incidence of neoplastic diseases has increased worldwide, with an estimated global burden of 19.3 million incident cases and 10 million deaths in 2020—a considerable increase compared with 9.6 million deaths in 2018. One of the most prevalent problems faced by patients with cancer and their physicians is malnutrition. It is estimated that patients with cancer have important nutritional alterations in 25% to 70% of cases, which directly affects many spheres of patient care and well-being, including quality of life, treatment toxicity, and survival outcomes. Despite the overwhelming need to address this pressing issue, current evidence in terms of pharmacologic interventions for cancer-related anorexia remains inconclusive, and there is no current standard of care for patients with cancer-related anorexia. Nonetheless, international guidelines recommend promoting anabolism through nutritional, physical, and pharmacologic therapies. In this review, the available information is summarized regarding pharmacologic therapies to treat cancer-related anorexia and findings are highlighted from a clinical stance.
Intergenerational high-fat diet impairs ovarian follicular development in rodents: a systematic review and meta-analysis
Authors: Paula Verônyca G , Vesentini Giovana , Sinzato Yuri K , Moraes-Souza Rafaianne Q , Volpato Gustavo T , Damasceno Débora C
Published: June 2021

Context

Excessive consumption of high-fat diets has increased in the population over time and is harmful to female fertility.

Objective

To investigate and discuss the effects of a high-fat diet on ovarian follicles in rodents.

Data source

A systematic literature search of PubMed, EMBASE, Web of Science, and SCOPUS was carried out.

Data Extraction

Study characteristics, including study design, population, intervention, outcome, and risk of bias were analyzed.

Data Analysis

Twenty-two articles were included in a systematic review. Given the availability of studies, a quantitative meta-analysis included 12 studies that were performed for outcomes. There was a decrease in primordial follicles in female rodents that received a high-fat diet compared with the standard diet group. The offspring of mothers exposed to a high-fat diet showed an increased number of cystic follicles and a decreased number of secondary follicles and antral follicles, compared with the control diet group. Therefore, these high-fat diet–induced follicular alterations might impair the fertility of dams and their female newborns.

Conclusion

The consumption of a high-fat diet causes damage to ovarian follicular development, and this commitment will persist in the next generation.

Systematic Review Registration

PROSPERO registration no. CRD42019133865.
Asian American Philosophy and Feminism
Authors: Kim David Haekwon
Published: June 2021

This chapter explores the intersection of Asian American philosophy and feminist philosophy. It considers feminist issues within Asian American philosophy and examines Asian American feminist philosophy as an important field in its own right that contributes to Asian American philosophy, feminist philosophy, and philosophy of race. The chapter starts with a brief discussion of reasons for including Asian American feminist philosophy in the profession and then elaborates a model for thinking about Asian America and Asian American philosophy, with particular consideration of xenophobic racism and Orientalist hypersexualization. The chapter then examines how Asian American feminist philosophy enriches our historical and social ontological understanding of American nation-building, reconceives important normative themes in philosophy of race, deepens our understanding of invisibility, and complicates our thinking about non-Eurocentric or decolonial feminist dialogue.
Analytical Feminist Ethics
Authors: Brennan Samantha
Published: June 2021

Feminist ethics is that branch of ethics that is concerned first and foremost with understanding the oppression of women and developing a normative analysis of its wrongness. Analytical feminist ethics uses the tools and techniques of analytical philosophy, such as conceptual analysis, to further understand the injustices revealed by feminist approaches to ethics. The chapter surveys analytic themes, trends, and tendencies within feminist ethics taking a broad lens on what counts. The chapter offers an account of central issues and themes in analytic feminist philosophical engagements with ethics, reflection on examples of important contributions to this discussion, a discussion the extent to which feminist work has changed or entered the mainstream of the field, and current and future directions in analytic feminist ethics.
Feminist Bioethics
Authors: Scully Jackie Leach
Published: June 2021

This chapter offers an account of the central issues and themes in feminist philosophical engagements with bioethics. After outlining the history and goals of feminist bioethics, I discuss how feminist ontology and epistemology have generated the distinguishing features of feminist bioethical approaches, including both the substantive topics addressed and the particular ethical areas highlighted. Among these areas are: attention to power dynamics and social context; the use of empirical information to inform ethical theory; a focus on relationality, care, and embodiment; and an acknowledgement of minority viewpoints that are often excluded from mainstream bioethics. In taking these distinctive approaches, feminist bioethics has also made major theoretical contributions to moral philosophy: here I discuss (i) the ethics of care and (ii) relational autonomy. Finally, I consider the extent to which feminist work has changed or entered the mainstream, and look to current and future directions in feminist bioethics.
The Body
Authors: Heyes Cressida J.
Published: June 2021

This chapter offers an overview of central issues and themes in feminist philosophical reflections on the body. It discusses at greater length three specific examples from recent debates in feminist philosophy: how concepts of sex and gender and their juxtaposition have been contested; how the phenomenological tradition has been reworked by critical feminist philosophers; and how feminist philosophers of disability challenge the reification of bodies, refocusing philosophical attention on bodies as always in process. All three debates provide complex and connected challenges to understandings of bodies as both natural and extra-cognitive, especially where these understandings imply that the body is not a proper subject for philosophy, or that the philosopher’s body is not relevant to their work.
Bias
Authors: Antony Louise
Published: June 2021

This chapter offers an account of central issues and themes in feminist philosophical reflections on bias and objectivity. Some feminists have argued that objectivity is an unachievable and thus inappropriate epistemic norm for human beings. But at the same time, these feminists have criticized philosophy for displaying masculinist bias. This complex critique faces a problem I’ve called the “Bias Paradox” and that Helen Longino calls an “Essential Tension:” how we can criticize partiality at the same time we acknowledge its ubiquity. I explain Longino’s proposed “social empiricist” solution, and contrast it with my own. I argue for a re-conception of “bias” as a normatively neutral epistemic inclination. Biases, in this sense, play a crucial constructive role in the development of human knowledge by solving the problem of underdetermination of theory by evidence. The biases we (correctly) regard as morally bad, such as social prejudice, involve the operation of neutral biases in unpropitious natural or social environments.
Prisons
Authors: Zurn Perry
Published: June 2021

This chapter offers an account of central issues and themes in feminist philosophical work on prisons, examples of important contributions, and future directions for feminist work in the field. It does so, however, in a way that consciously deploys a feminist methodology that resists the replication of hierarchical norms and structural violence in the very doing of theory and history. In this spirit, it emphasizes the record of struggle across the prison’s history, the resistance efforts that live behind individual academic theories, and the conceptual frameworks generated by groups bearing the brunt of carcerality, and it investigates alternative strategies of harm reduction developed across those communities. The chapter closes with an explicit exploration of prison abolitionism, which works not only to radically rethink punishment but also to shift the locus of voice and leadership. In so doing, the chapter aims to review, as much as to create anew, a feminist theoretical analysis of prisons.
Feminist Critical Theory
Authors: Weir Allison
Published: June 2021

This chapter offers an account of central issues and themes in feminist philosophical engagements with critical theory, focusing specifically on critical theory of the Frankfurt School. The chapter’s discussion reflects on examples of important feminist interventions in and contributions to critical theory, debates within feminist critical theory, and the extent to which critical theory can be considered feminist given its critique of power relations and interests in emancipation. The chapter suggests that future directions in the field must go beyond the question of gender inclusion and focus on the transformation of critical theory itself.
Biomedical Technologies
Authors: Dodds Susan
Published: June 2021

This chapter focuses on feminist philosophical engagement with biomedical technologies, such as the development of in vitro fertilisation (IVF), genetic engineering, bionic implants, neural interventions, and synthetic biology. The chapter starts with a short account of the contemporaneous rise of bioethics as a subdiscipline of philosophy, a range of emerging biomedical technologies and the second wave of feminist political action and theory. It outlines some key feminist philosophical approaches to issues in biomedicine: including those focusing on autonomy and choice; care and care work; and the moral significance of narrative, embodiment and phenomenological experience. It ends by identifying some evolving future directions for feminist philosophical contributions to emerging technologies informed by discussion of vulnerability and dependence; disability, neural diversity, and human enhancement.
Feminism and Disability Theory
Authors: Carlson Licia
Published: June 2021

This chapter maps out connections between feminist and disability theories to bring into relief the multiple ways that feminist philosophers are partaking in these conversations. It begins with a discussion of what is distinctive about feminist approaches to disability, while recognizing that there is not a single, univocal “feminist philosophy of disability.” It then turns to specific areas of philosophical inquiry in which feminist philosophers address disability, including ontological, epistemological, political, ethical, and bioethical considerations. The final section highlights a number of themes central to work in feminist philosophy and disability: embodiment, identity, intersectionality, and the generative and positive dimensions of disability. The chapter concludes by pointing to more recent directions in feminist philosophy of disability. These include disability aesthetics, explorations of disability in the context of technoscience and ecofeminism, and the problem of ableism in philosophy and the academy more broadly.
Animal Studies
Authors: Gruen Lori
Published: June 2021

Animal studies is a rapidly developing interdisciplinary field. It has roots in both animal ethics and feminist philosophy. While mainstream animal ethics has not yet incorporated the insights from feminist philosophy, work in animal studies has increasingly drawn on and built upon feminist thinking. Feminist animal studies can, in turn, contribute to discussions in feminist ethics and feminist epistemology. In this chapter, three key connected issues that are central to feminist philosophy and important within animal studies are discussed: the centrality of relationships, navigating difference, and speaking for others.
Poststructuralism
Authors: Kolozova Katerina
Published: June 2021

This chapter offers an account of central issues and themes in feminist philosophical engagements with poststructuralism, reflection on examples of important contributions to this discussion, a discussion of the extent to which feminist work has engaged and critiqued the mainstream of the field, and feminist poststructuralist theorizations of the subject, identity, and culture. It also offers a critical genealogy of the epistemological paradigm poststrustructuralism has come to represent, in search of its continuities and breaks from its foundations furnished by French structuralism, psychoanalysis and tangential links with Marxian critical theory. It argues that the anglophone appropriations of structuralism in postmodern context, as it would have been termed in the French academe, have veered away from the original and purely formal conceptualization of the subject by resorting to what might be called, in Marxian terminology, identity centered reifications. This chapter puts forward the claim that poststructuralist discourse and the neoliberal discourse of individual and social mobility, transformativity and the concomitant proclamation of “the death of ideology” (and history) have established numerous and mutually opportune discursive and ideological correspondences.
Immediate Improvements in Patellofemoral Pain Are Associated With Sagittal Plane Movement Training to Improve Use of Gluteus Maximus Muscle During Single Limb Landing
Authors: Atkins Lee T , James C Roger , Yang Hyung Suk , Sizer Phillip S , Brismée Jean-Michel , Sawyer Steven F , Powers Christopher M
Published: June 2021

Objective

The authors sought to examine the immediate effects of movement training aimed at improving use of gluteus maximus (GMAX) in the sagittal plane on hip internal rotation and self-reported patellofemoral pain (PFP) during single-limb landing.

Methods

Seventeen females with PFP participated. Lower extremity kinematics and kinetics, GMAX activation, and self-reported PFP were obtained before and after a single-session movement training program aimed at increasing the use of GMAX. Dependent variables of interest included self-reported PFP, average GMAX activation, average hip extensor moment, and peak hip internal rotation. Post-training changes were evaluated using paired t tests and Wilcoxon signed rank tests.

Results

Following movement training, self-reported PFP decreased significantly (mean [standard deviation]) (3.9 [1.1] vs 0.8 [1.3] on a 0–10 scale). Additionally, significant increases were observed for the average hip extensor moment (0.6 [0.3] vs 1.8 [0.4] Nm/kg) and average GMAX activation (41.0% [18.3] vs 51.6% [25.7] maximum voluntary isometric contraction), whereas peak hip internal rotation decreased significantly (8.5 degrees [5.8] vs 6.0 degrees [5.3]).

Conclusion

Movement training aimed at improving the use of GMAX in the sagittal plane resulted in clinically relevant changes in self-reported pain, GMAX activation, and hip kinetics and kinematics. Improving the use of GMAX during movement merits consideration when designing rehabilitation programs for females with PFP.

Impact

The current study highlights the clinical utility of movement training for persons with PFP and provides a biomechanical rationale for its use as a potential intervention in this population.
A clinical perspective on lifelong deglutition: What do we do when it does not work?
Authors: Skoretz Stacey A.
Published: June 2021

Swallowing and breathing are two vital processes necessary to sustain human life. These acts require precise coordination given their biomechanical interdependence as characterized by their shared anatomy, neurophysiological regulation and function (Miller, Bieger, & Conklin, 1997; Shaw & Martino, 2013). Whether or not a swallow is competent is governed not only by the integrity of its anatomy but also by multiple factors including those that are: systemically mediated, part of the external environment or any combination thereof. As a result, the traditional swallowing phases, as they evolve over the lifespan of an individual, are best understood by taking a cross‐systems perspective (Martin‐Harris, Brodsky, et al., 2005; Matsuo & Palmer, 2009). This approach is the cornerstone of innovative assessment and management techniques for oropharyngeal dysphagia (or disordered swallowing), which supports subdivisions of the swallowing phases. This modern perspective affords the opportunity to ascertain the subtleties of the swallow's anatomical symbiosis with other processes, its intricate physiology all while opening the door to novel dysphagia intervention. This session will: 1) outline the anatomical and physiological differences between reflexive and volitional swallows, 2) explore a cross‐systems approach to understanding swallowing anatomy and physiology across the lifespan, and 3) review clinical cases that highlight the importance of anatomical and biomechanical integrity during swallowing.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Neovascularization in Pancreatic Cancer is Dependent on Neuropilin 2
Authors: Destin Orlane , Niclou Benoit , Li Xiaoran , Levonyak Nicholas , Jia Amy , Watnick Randy S. , Adam Rosalyn M. , Bielenberg Diane R.
Published: June 2021

Pancreatic ductal adenocarcinoma (PDAC) has a high mortality rate due to lack of detection, tendency to metastasize to the liver, and the absence of effective treatments. Consequently, there is an urgent need to understand the biology of this devastating disease in order to develop drugs to inhibit PDAC progression. Neuropilin‐2 (Nrp2) is a transmembrane receptor that binds competitively to either the angiogenic ligand, Vascular Endothelial Growth Factor (VEGF), or the inhibitory protein, Semaphorin‐3F (SEMA3F). Nrp2 expression is quiescent in the normal adult blood vasculature, however the expression of Nrp2 is strongly upregulated in tumor‐associated neovessels in human and mouse xenograft models of PDAC. Nrp2‐deficient mice in the C57BL/6J background are viable with no obvious defects in the blood vascular system or signs of edema. Using immunohistochemistry to CD31, we compared the blood microvascular density (MVD) in the adult mouse pancreas of Nrp2+/+ wildtype mice and Nrp2−/− knockout (KO) mice and found no significant difference. However, when luciferase‐labeled syngeneic PDAC cells were injected orthotopically into the pancreas of Nrp2‐mutant mice, subsequent PDAC tumor growth was impeded in mice lacking Nrp2 compared to wildtype littermates. Additionally, PDAC tumors showed reduced tumor MVD in Nrp2‐deficient mice compared to PDAC tumors in Nrp2 wildtype littermates. Correspondingly, the incidence of liver metastasis was inhibited in mice lacking Nrp2 suggesting that tumor angiogenesis and metastasis is dependent on endothelial expression of Nrp2 in this PDAC model. Lastly, PDAC tumor cells do not express the VEGF Receptor 2 tyrosine kinase and therefore do not respond in vitro to VEGF stimulation. However, the Nrp2 inhibitory ligand, SEMA3F, was able to directly inhibit the migration of PDAC tumor cells in vitro. Taken together, our data suggests that Nrp2 may be an important receptor to target in both tumor cells and endothelial cells in PDAC. Our results suggest that targeted therapy to the NRP2 axis could be a potential treatment strategy to inhibit the growth and metastasis of pancreatic tumors.

Support or Funding Information

NIH CA155728 (DRB)

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
RAGE and SAGE: Ameliorating COPD Pathogenesis via RAGE Abrogation
Authors: Hirschi Kelsey M , Tsai K YF , Davis T , Llavina S , Stitton B , Clark C , Plothow E , Aanderlund‐Tanner H , Mella N , Arroyo J A , Reynolds P R
Published: June 2021

Chronic obstructive pulmonary disease (COPD) is a progressive lung disease involving chronic airway inflammation and emphysema. While primary smoke poses the greatest risk, evidence suggests nearly half of the US population is also at risk due to exposure to second hand smoke (SHS). In the present study, we used control, RAGE null, and lung‐specific RAGE overexpressing transgenic (TG) mice to study the role of RAGE during responses to SHS. We evaluated inflammatory effects of SHS in these mice with and without the administration of semi‐synthetic glycosaminoglycan ethers (SAGEs), a family of anionic, partially lipophilic sulfated polysaccharide derivatives known to inhibit RAGE signaling. Mice were weaned and fed doxycycline to induce RAGE in TG mice at PN30. Select mice were exposed to SHS from three Kentucky 3R4F research cigarettes via a nose‐only delivery system (Sireq Scientific, Montreal, Canada) five days a week and ip injections of PBS or SAGE (a 30mg/kg body weight) occurred three times per week from PN40‐70 before all mice were sacrificed on PN70. RAGE mRNA and protein expression was elevated following SHS exposure of control and TG mice and no expression was detected in RAGE null mice. Bronchoalveolar lavage fluid (BALF) analysis revealed RAGE‐mediated influence of inflammatory cell diapedesis and BALF protein abundance. A multiplex cytokine array was performed in order to precisely determine the secretion of pro‐inflammatory modulators into BALF. Lung histological assessment revealed indistinguishable morphological changes following exposure, yet apoptosis was increased in lung parenchyma. Thematically, inflammatory signaling intermediates and downstream responses induced by SHS exposure were influenced by the availability of RAGE, as evidenced by RAGE nulls and SAGE treatment. These data reveal fascinating data suggesting therapeutic potential for the use of RAGE inhibitors in lungs exposed to SHS smoke.

Support or Funding Information

This work was supported by a grant from the Flight Attendant's Medical Research Institute (FAMRI, PRR and JAA) and a BYU Mentoring Environment Grant (JAA and PRR).

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
What can trabecular bone tell us about activity levels and self‐domestication?
Authors: Chirchir Habiba
Published: June 2021

Various studies have compared trabecular bone fraction (i.e., TBF both volumetric and areal) among modern humans, great apes and fossil hominins and found that modern humans have gracile skeletons in having low TBF. This has been observed even among populations engaging in greater levels of activity such as foraging compared to farming. These findings raise questions about when and why the gracile human skeleton emerged. Although, sedentism has been proposed to explain this phenomenon, another hypothesis that may explain the unusually gracile modern human skeleton is the human self‐domestication (HSD) hypothesis. This hypothesis proposes that selection for prosociality among mammals with increased cognition resulted in changes in morphological features e.g., having a slight reduction in cranial capacity, a globular cranium, and thin cranial bones. In fact, other mammals thought to have undergone self‐domestication such as bonobos vs. chimpanzees, domestic dogs vs. wolves exhibit this trend in prosociality, and display differences in morphological traits such as feminization of the skull, and a reduction in cranial capacity among others. Thus, these observations provide an opportunity to test the HSD hypothesis. The present study tests this hypothesis first, by examining whether domestic dogs have low TBF (gracile skeletons) compared to their wild relatives: the wolves, foxes, and coyotes based on the understanding that domestic dogs are prosocial relative to their wild counterparts and therefore, would exhibit low TBF as a by‐product of selection for prosociality. Secondly, by estimating TBF in the human fossil record comparing hominins from the Pleistocene (early Homo and upper Paleolithic Homo), and recent modern humans from the Holocene. MicroCT and pQCT scanning were used to image proximal femora and humeri, which were then analyzed using Quant3D to quantify TBF. One‐way ANOVA with Tukey post‐hoc correction was used to identify differences among species. Results show that, indeed the domestic dogs across breeds studied exhibit low TBF compared to wolves and other canids. Secondly, that recent modern humans have low TBF compared to Pleistocene hominins. These results suggest that it is plausible that apart from sedentism, selection for prosociality may have had an effect on gracility, however, more work on other prosocial species that underwent self‐domestication needs to be done to further test this hypothesis and better understand the mechanisms responsible for it. These findings indicate that the highly gracile skeletons of modern humans and the increased risks of bone fracture associated with a decline in bone mass have evolutionary underpinnings‐ albeit relatively recent‐ than has been considered before.

Support or Funding Information

NASA WV Space Consortium

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Connexin Gap Junction Proteins in Development and Disease
Authors: Laird Dale W
Published: June 2021

Connexins form tightly‐regulated large‐pore channels that facilitate the passage of various ions, metabolites, and signaling molecules directly between cells, or in some cases and/or pathologies, to the extracellular milieu. The human connexin encoding gene family consists of 21 members and mutations in half of these genes leads to over two dozen diseases ranging in severity from manageable developmental abnormalities to life‐shortening organ failure. Developmentally, connexin expression and gap junctional intercellular communication begins at the 8 cell stage and persists throughout organogenesis resulting in most adult cells expressing two or more connexin subtypes. Connexin genes are exquisitely regulated during all developmental processes before birth, and in many tissues like the skin, after birth. Connexins regulate their function by channel gating processes and notably through their turnover owing to their short half‐life of only a few hours. Given their ubiquitous distribution it is not at all surprising that gene mutations lead to disease. In fact, it is probably more surprising that patients harbouring connexin gene mutations do not present with more clinical morbidities. Our laboratory has used tissue‐relevant cells, primary cells, organotypic cultures, mouse models of human diseases, and induced pluripotent stem cells from connexin‐linked disease patients to uncover ten distinct mechanisms by which connexin gene mutations cause disease. Collectively, connexin‐disease linked mutants have been classified into distinct gain‐ and loss‐of function molecular mechanisms of action. Our long‐term goals include developing strategies to compensate or overcome the cellular and tissue defects triggered by these mutants. This presentation will discuss how connexins have emerged as therapeutic targets in disease and in injury repair. We anticipate that once it is better understood how connexin gene mutations cause disease and abnormalities, which often present more acutely during aging, these findings could be translated into pre‐clinical studies leading to possible treatments for gap junction‐linked diseases.

Support or Funding Information

Supported by the Canadian Institutes of Health Research.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Human cortical organoids from single iPSC‐derived neural rosettes for studying human cortical development and disorders
Authors: Shcheglovitov Alex , Wang Yueqi , Bell Laura , Russell Chad , Armstrong Celeste , Spampanato Jay
Published: June 2021

Human cerebral cortex is the most complex brain structure implicated in many human‐specific behaviors and disorders. Genes important for the development and wiring of human cortex have often been found mutated in individuals with neurodevelopment disorders. Cerebral organoids generated from human embryonic and induced pluripotent stem cells have been used for modeling human‐specific aspects of cortical development; however, some variability‐ and maturation‐related issues prohibit the widespread use of these approach for disease modeling. We developed a new protocol for growing human cortical organoids from single stem cell‐derived neural rosettes and demonstrated that single‐rosette‐derived cortical organoids grow large in suspension culture, reaching 4–5 mm in diameter by 4 months, and consist of different types of properly organized neuronal cells, including cortical neural progenitors, deep and superficial cortical excitatory neurons, inhibitory neurons, and astrocytes. Using slice patch‐clamp electrophysiology, we show that many neurons in slices from single‐rosette‐derived cortical organoids fire repetitive action potentials, receive excitatory and inhibitory synaptic inputs, exhibit typical pyramidal‐like morphologies, and have dendritic spines. Our results indicate that single‐rosette‐derived cortical organoids can be used as a more robust experimental system for modeling human cortical development and disorders.

Support or Funding Information

Utah Neuroscience Initiative Seed Grant, Whitehall Foundation, Brain Research Foundation, Brain and Behavior Research Foundation, NIMH, NINDS

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Discovery of Novel Mechanisms for Idiopathic Pain Disorders Through Genome Wide Approaches
Authors: Smith Shad B.
Published: June 2021

This presentation will introduce an overview of recent findings of genetic variants associated with chronic pain, focusing on recent discoveries from a large cohort study of painful temporomandibular disorders (TMD), the leading cause of orofacial pain. The Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) study was designed to identify risk factors for development of TMD. Recognized as a complex condition with biological and psychosocial risk factors, TMD has also been shown to have a substantial genetic component. Dr. Smith will discuss genome‐wide and bioinformatics approaches that have revealed etiological mechanisms underlying TMD, representing novel pathways of vulnerability. This work has implicated genetic variation associated with the presence of chronic pain, as well as polymorphisms associated with intermediate phenotypes known to be major risk factors for TMD development. Data from stratified analyses indicate certain pathways may be distinct between sexes. To understand the functional significance of these novel discoveries, additional behavioral and bioinformatics studies have been performed that show convergent lines of evidence pointing to immunological as well as neurological mechanisms. The state of knowledge about genetic contributors to orofacial pain and its management will be summarized with an emphasis on how these findings may be applied for personalized and targeted treatment of pain.

Support or Funding Information

This work was supported by the National Institute of Dental and Craniofacial Research (NIDCR) grant number U01DE017018, and by a K12 Biomedical Researcher Development Scholarship in TMJD and Orofacial Pain (K12DE022793).

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Populations from under‐represented backgrounds are not adequately represented in clinical databases
Authors: Barnes Kathleen
Published: June 2021

Personalized medicine (PM) is a field in medicine that leverages information about a patient's genes, environment and behavior to prevent, diagnose, and treat disease. Health care providers rely on publicly available genetic databases for recommendations for implementing PM. For example, the Clinical Pharmacogenetics Implementation Consortium (CPIC) makes recommendations for clinical implementation of pharmacogenetics tests by creating, curating, and sharing peer‐reviewed, evidence‐based and updated drug‐gene pair clinical practice guidelines. While most drugs with CPIC guidelines have at least some evidence based off of non‐European data, none have been exclusively developed for a specific ancestral group. Similarly, ClinVar, an NIH supported, freely accessible archive, reports relationships between genetic variation and disease phenotypes. However, these databases reflect a measurable bias toward genetic data based on European ancestry, owed in large part to the underrepresentation of non‐white populations in federally funded and published research programs, including genome wide association (GWAS) and whole genome sequencing studies, which in turn limits the ability to identify variants associated with disease and response to certain therapeutics. Inadequate representation further exacerbates existing health disparities. After over a decade of GWAS, non‐European, non‐Asian groups combined account for <4% of individuals represented in the international GWAS catalog. Previously the role that ancestry plays in variant prioritization approaches often implemented in genomic medicine (e.g., Human Gene Mutation Database, ClinVar) was explored and it was determined these databases are missing considerable African‐specific pathogenicity data. Recent developments through national and international initiatives have provided an opportunity to classify new genetic variants and reassess prior variant classifications and deposit this information into public databases. Approximately half of the NHLBI supported Trans‐Omics for Precision Medicine (TOPMed) program's samples represent non‐European samples. Similarly, the NHGRI Population Architecture using Genomics and Epidemiology (PAGE) study aims to better characterize how genetic factors influence susceptibility to disease in a multi‐ethnic dataset. Researchers representing both TOPMed and PAGE previously designed a commercially available multi‐ethnic genotyping array that was enriched with genetic variants representing underrepresented minority populations, which is being widely used, including institutional biobanks. Together, these developments promise to improve genomic diversity and subsequently benefit underrepresented minorities through personalized medicine.

Support or Funding Information

NIH grant #HL104608

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
To Code or Not to Code: What Is the Linc?
Authors: Flavell Richard
Published: June 2021

The annotation of the mammalian protein coding genome is incomplete. Arbitrary open reading frame (ORF) size restriction and the absolute requirement for a methionine codon as the sole initiator of translation, have constrained identification of potentially important transcripts with non‐canonical protein coding potential. Using unbiased transcriptomic approaches in macrophages responding to bacterial infection, we show widespread ribosome association with a large number of RNAs that were previously annotated as “non‐protein coding”. Although the ability of such non‐canonical ORFs to encode functional protein is controversial, we identify a plethora of novel short and non‐ATG initiated ORFs with the ability to generate stable and spatially distinct proteins. Importantly, we show that the translation of a novel ORF ‘hidden’ within the long non‐coding RNA Aw112010 is essential for the orchestration of mucosal immunity during both bacterial infection and colitis. Together this work expands our interpretation of the protein coding genome and demonstrates the critical nature of proteinaceous products generated from non‐canonical ORFs to the immune response in vivo. We therefore propose that the misannotation of non‐canonical ORF‐containing genes as non‐coding RNAs may obscure the essential role of a multitude of previously undiscovered protein coding genes in immunity and disease.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Fractional‐nucleotide translocation in sequence‐dependent pausing by RNA polymerase: Single‐molecule picometer‐resolution nanopore tweezers (SPRNT)
Authors: Ebright Richard , Nova Ian , Yang Shuya H. , Mazumder Abhishek , Laszlo Andrew , Derrington Ian , Gundlach Jens
Published: June 2021

Single‐molecule picometer‐resolution nanopore tweezers (SPRNT) enables monitoring of translocation of a nucleic‐acid motor protein on a nucleic‐acid track with sequence registration, sub‐nucleotide spatial resolution, sub‐millisecond temporal resolution, and the ability to apply assisting and opposing forces.

We have demonstrated the ability of SPRNT to monitor translocation of RNA polymerase (RNAP) relative to the DNA template strand, the DNA non‐template strand, and the RNA product strand in transcription, and we have applied SPRNT to analyze RNAP translocation in transcription elongation and sequence‐dependent transcriptional pausing.

The results show that sequence‐dependent transcriptional pausing involves a “half‐translocated” state in which RNAP translocates relative to the DNA template strand by 0.5 nucleotides. The “half‐translocated” state is unable to bind the next NTP substrate, presumably because RNAP translocation by 0.5 nt does not align the next template‐strand nucleotide with the RNAP active‐center NTP addition site. The half‐translocated state interconverts rapidly (~0.1–1 s) with the “pre‐translocated” state and converts slowly (~1 s) to the NTP‐binding‐competent “post‐translocated state.” In the presence of saturating NTPs, conversion to the post‐translocated state is followed by pause escape. In the presence of limiting NTPs, conversion to the post‐translocated state is followed by return to interconverting half‐translocated and pre‐translocated states and continued pausing.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH
Authors: Cai Long , Shah Sheel , Tekei Yodai , Zhao Wen , Lubeck Eric , Yun Jina , Eng Chee‐Haut Linus , Koulena Noushin , Cronin Christopher , Karp Christopher , Liaw Eric J. , Amin Mina J.
Published: June 2021

Visualization of the transcriptome and the nuclear organization in situ in individual cell is the holy grail of single cell analysis. Here, we demonstrate a multiplexed single molecule in situ method, intron seqFISH, that allows imaging of 10,421 genes at their nascent transcription active sites in single cells, followed by mRNA and lncRNA seqFISH and immunofluorescence. This nascent transcriptome profiling method can identify different cell types and states with mouse embryonic stem cells and fibroblasts. The nascent sites of RNA synthesis tend to be localized on the surfaces of chromosome territories and their organization in individual cells is highly variable. Surprisingly, the global nascent transcription oscillated asynchronously in individual cells with a period of 2 hours in mouse embryonic stem cells as well as in fibroblasts. Together, spatial genomics of the nascent transcriptome by intron seqFISH reveals nuclear organizational principles and fast dynamics in single cells that are otherwise obscured.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Retinol Binding Protein 4 (RBP4) in Adipocytes and Obesity
Authors: Shmarakov Igor , Lee Seung‐Ah , Blaner William S.
Published: June 2021

We have earlier reported the generation and study of transgenic mice that express human RBP4 (hRBP4) in both white and brown adipocytes (Lee et al. Hepatology 2016, 64:1534–1546). Our published studies of these mice (adi‐hRBP4 mice) established that white adipocyte expression RBP4 induces inflammation in white adipose tissue (WAT) that is responsible for the hepatic steatosis phenotype seen in chow fed adi‐hRBP4 mice. When maintained on a high fat diet, adi‐hRBP4 mice gain significantly more body weight than matched control mice. We have investigated the basis for this weight gain phenotype and found that this involves marked RBP4‐induced changes in brown adipose tissue (BAT) physiology. H&E stained BAT obtained from adi‐hRBP4 mice shows the presence of large unilocular lipids in brown adipocytes. Biochemical measures establish that there is elevated triglyceride accumulation in BAT of adi‐hRBP4 mice that is accompanied by increased expression in BAT of genes involved in triglyceride synthesis. In addition, BAT from adi‐hRBP4 mice shows diminished expression levels for genes involved in BAT identity and function. Most importantly, uncoupling protein‐1 (UCP1) mRNA and protein levels are markedly reduced. This is accompanied by significantly diminished BAT levels of all‐trans‐retinoic acid. In vitro studies involving the use of mouse embryonic fibroblasts (MEFs) obtained from adi‐hRBP4 and matched control mice as well as brown and white stromal vascular cells induced to differentiate to adipocytes, confirmed that RBP4 expression in brown adipocytes alters gene expression patterns in the differentiated adipocytes. Collectively, our data suggest that elevated RBP4 expression in BAT effects all‐trans‐retinoic acid‐mediated processes giving rise to a whitening of BAT and diminished BAT actions. We propose that this underlies the weight gain phenotype we have observed.

Support or Funding Information

Supported by NIH grants R01 DK068437 and R01 DK101251

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.