Human Biology Research Research Articles

Abstract A022: Patho-DBiT: Spatially exploring RNA biology in archival formalin-fixed paraffin- embedded tissues

Abstract Despite recent breakthroughs in spatial biology, either imaging-based or sequencing-based spatial transcriptomics is largely equivalent to spatial messenger RNA (mRNA) expression quantification. An RNA molecule experiences a complex life cycle involving transcription, splicing, maturation, translation, and degradation . It is highly desirable to profile all these RNA species spanning their life cycle to explore the biology of RNA at genome scale and cellular level. Furthermore, formalin-fixed paraffin-embedded (FFPE) tissues are essential in clinical practice, being the backbone of human disease histopathological diagnoses . Pathology departments have accrued vast collections of FFPE blocks over time, creating a rich, yet underutilized compendium of materials that, accompanied by clinical data, stands as a treasure trove for human biology and translational research . In this evolving landscape, we present “Pathology-compatible Deterministic Barcoding in Tissue” (Patho-DBiT) not only enabling spatial full-coverage base-by-base whole transcriptome sequencing but also crafted to address the challenges of clinically archived FFPE tissues. Patho-DBiT integrates in situ polyadenylation, microfluidic in tissue barcoding, and computational innovations to decode rich RNA biology inherent in FFPE samples. The platform capitalizes on RNA fragmentation naturally occurring in FFPE specimens and appends poly(A) tails to a broad spectrum of RNA species, thereby overcoming traditional barriers associated with FFPE samples and even outperforming the assays conducted with frozen tissues. Patho-DBiT permits spatial co-profiling of gene expression and alternative splicing, unveiling region-specific isoforms in the mouse brain. High-sensitivity transcriptomics is constructed from 5-year archived T-cell lymphoma tissues, with cross-validation conducted using super-resolution spatial phenotyping technology (CODEX). Furthermore, genome-scale single nucleotide RNA variants (SNVs) are captured to distinguish malignant subclones from non-malignant cells in human B-cell lymphomas, dissecting spatial clonal architectures based on both SNVs and copy number variation (CNV) profiles. Patho-DBiT also enables spatially resolved co-profiling of large and small RNAs, facilitating the analysis of a microRNA-mRNA regulatory network and tRNA utilization within clinical biopsies and elucidating their roles in tumorigenesis. With superior intronic read capture efficiency, Patho-DBiT spatially mapped RNA splicing dynamics associated with the developmental trajectory of tumor B cells. High resolution Patho-DBiT with a 10-μm spot size reveals the heterogeneities of human lymphomas within a spatial neighborhood and traces the spatiotemporal molecular kinetics driving tumorprogression at the cellular level. Patho-DBiT represents a first-of-its-kind technology, enabling the spatial exploration of rich RNA biology in FFPE tissues to aid in clinical pathology research. Citation Format: Zhiliang Bai, Dingyao Zhang, Yan Gao, Bo Tao, Mingyao Li, Yi Xing, Jun Lu, Mina Xu, Rong Fan. Patho-DBiT: Spatially exploring RNA biology in archival formalin-fixed paraffin- embedded tissues [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A022.

Conducting Human Biology Research Using Invasive Clinical Samples: Methods, Strengths, and Limitations.

Invasive biological samples collected during clinical care represent a valuable yet underutilized source of information about human biology. However, the challenges of working with clinical personnel and the invasive nature of sample collection in biomedical studies can hinder the acquisition of sufficiently large sample sizes for robust statistical analyses. In addition, the incorporation of demographic data from participants is crucial for ensuring the inclusiveness of representative populations, identifying at-risk groups, and addressing healthcare disparities. Drawing on both research experiences and the existing literature, this article provides recommendations for researchers aiming to undertake efficient and impactful projects involving invasive human samples. The suggested strategies include: (1) establishing productive collaborations with clinicians; (2) optimizing sample quality through meticulous collection and handling procedures; and (3) strategically implementing a retrospective model to capitalize on existing invasive sample repositories. When established, cooperative work between clinical health care workers and biological anthropologists can yield insights into human biology that have the potential to improve human health and wellbeing.

Blood Sampling and Hormone Measurement for Determining the Stage in the Ovarian Cycle in Marmosets.

Common marmosets are small New World monkeys. Since many of their biological mechanisms are similar to those of humans, marmosets are potentially useful for medical and human biology research across a range of fields, such as neuroscience, regenerative medicine, and development. However, there is a lack of literature describing methods for many basic experiments and procedures. Here, detailed methods for determining the levels of sex hormones (progesterone, estradiol, and chorionic gonadotropin) in marmosets are described. The measurement of these hormones enables the prediction of the stage in the ovarian cycle, which is typically 26-30 days in marmosets; accurate determination is essential for the harvesting of oocytes/zygotes at the correct time point and for the preparation of host females for the generation of genetically modified marmosets. Additionally, the measurement of sex hormone levels is useful for endocrinology, ethology, early development, and reproductive biology studies. This protocol provides a detailed description of the methods for blood sampling from the femoral vein, separation of plasma for hormone measurement, measuring chorionic gonadotropin levels using urine and plasma, resetting the ovarian cycle using injections of a prostaglandin F2α analog to shorten and synchronize the cycle, and promoting follicular growth and ovulation by injecting follicle-stimulating hormone and chorionic gonadotropin. Using these protocols, the stages in the ovarian cycle can be determined for the timely collection of oocytes/zygotes.

Why religion and spirituality are important in human biological research.

The study of human biology includes exploration of all the genetic and environmental influences on human variation and life history, including impacts of sociocultural and physical environments. Religious practice and spirituality may be one of these influences. There are more than 5.8 billion religiously affiliated adults and children, accounting for 84% of the world's 6.9 billion people. Furthermore, 70% of Americans consider themselves spiritual in some way, including 22% who do not consider themselves religious, and the numbers for Europe are lower but proportionally similar. Such a high rate of religious affiliation and spiritual belief suggests that religion and spirituality could be sociocultural influences on human variation, but human biologists have scarcely attended to their impacts, as indicated by the limited numbers of relevant articles in the two flagship human biology journals. In this article, we discuss why human biologists may have overlooked this important force for human variability and highlight foundational work from human biology and other disciplines that can give our colleagues directions forward. We review the impacts of religion and spirituality at population and individual levels and call for human biologists to attend to the many aspects of religion and spirituality that can impact human biology and are much more than simply influences of denominational affiliation.

Microbiome and cancer: from mechanistic implications in disease progression and treatment to development of novel antitumoral strategies.

Cancer is a very aggressive disease and one of mankind's most important health problems, causing numerous deaths each year. Its etiology is complex, including genetic, gender-related, infectious diseases, dysbiosis, immunological imbalances, lifestyle, including dietary factors, pollution etc. Cancer patients also become immunosuppressed, frequently as side effects of chemotherapy and radiotherapy, and prone to infections, which further promote the proliferation of tumor cells. In recent decades, the role and importance of the microbiota in cancer has become a hot spot in human biology research, bringing together oncology and human microbiology. In addition to their roles in the etiology of different cancers, microorganisms interact with tumor cells and may be involved in modulating their response to treatment and in the toxicity of anti-tumor therapies. In this review, we present an update on the roles of microbiota in cancer with a focus on interference with anticancer treatments and anticancer potential.

More than Ethics: Changing Approaches to Research in Human Biology

Work in biological anthropology and human biology that engages with, extracts, manipulates, analyzes, and disseminates biological data from and associated with people requires serious ethical investment as central to method, theory, and practice. However, ethics is not enough. Moving beyond a call for better (or more) ethics, there is a core need for anthropological, historical, antiracist/anticolonialist method and theory in dealing with human data (existing, newly collected, and future collections). But there are structures in the academy, historical, financial, hierarchical, discriminatory, that impede sincere and effective actions to make such changes. Encouragingly, calls for structural change and some actions entailing it are under way. But individual efforts are not enough—systemic, profession-level processes need to be addressed.

Embodiment, Plasticity, and the Re/Production of Gender, Sex, and Race in Human Biology

abstract: This article historically situates human biology research by engaging with feminist science and technology scholars to show plasticity, how a key mechanism of embodiment, is used to re/produce sex and gender binaries in anthropological research and beyond. It first defines embodiment and demonstrates its reliance on plasticity and then reviews how and why plasticity has been taken up in human biology research. The article then engages with the works of feminist, trans, and queer scholars who have examined the connections among embodiment, plasticity, and the creation of Western binarized sex and gender. Further, the article presents how the re/production of a sex and gender binary is entwined with the justification of racial hierarchies through plasticity. While deterministic frameworks are often the most criticized in biology for harmful racist and sexist understandings of race and gender, plasticity and gene × environment interaction frameworks are not without fault. Even with large shifts in scientific understanding—in this case, from determinism to plasticity—science, in particular human biology, can still be a tool to create and maintain racist, patriarchal, cis- and heteronormative systems. The author concludes with recommendations and possible pathways forward for embodiment and plasticity research in human biology, suggesting that human biology research should engage with feminist science and technology critiques to be mindful of how our concepts might be re/producing harm.

SEBP_HNHC: Stacking Ensemble-based Bi-level Predictor for Human Non-Histone Crotonylation combining with iterative feature representation strategy

Accurate identification of crotonylation on human non-histone sites plays a crucial role in human biological research. Compared with traditional experimental methods that are labor-intensive and time-consuming, computational methods are more and more popular in recent years. Most of previous research methods are only for the prediction of crotonylation sites of histones, and there is a lack of targeted prediction tools for the identification of crotonylation sites of human non-histone proteins. In this study, we propose a stacking ensemble-based bi-level predictor for human non-histone crotonylation combining with iterative feature representation strategy, named SEBP_HNHC. To take full advantage of all the training information and solve the extreme imbalance between positive samples and negative samples, we propose a two-layer training data structure including preliminary training dataset and balanced training dataset. Preliminary training dataset is firstly divided into twelve subset using a special data division method. Then, multi-view feature encoding schemes are integrated to comprehensively represent the attribution of samples in each training subset. Next, Gini index combined with sequential forward search is employed for feature optimization for each preliminary training subset. Then, 84 preliminary models are built based on seven kinds of classifiers for twelve preliminary training subset that are now more commonly used and efficient. And then, a balanced training dataset is utilized to synthesize the capabilities of 84 preliminary models by generating 84 probability values as 84-D features for stacking ensemble. Finally, deep ensemble features are mined through iterative feature representation strategy. The experiment results show that the SEBP_HNHC method achieves robust performance in crotonylation sites prediction. Therefore, SEBP_HNHC is an effective tool for identification of crotonylation on lysine sites in human non-histone proteins.

Special Issue: Spatial Omics

GEN BiotechnologyVol. 2, No. 2 Call for PapersFree AccessSpecial Issue: Spatial OmicsDeadline for Manuscript Submission: June 15, 2023Guest Editors: Rong Fan and Omer BayraktarGuest Editors: Rong FanYale UniversitySearch for more papers by this author and Omer BayraktarWellcome Sanger InstituteSearch for more papers by this authorPublished Online:18 Apr 2023https://doi.org/10.1089/genbio.2023.29076.cfp2AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Single-cell omics has revolutionized biological and biomedical research in the past decade despite the inability to measure single cells in the tissue context. Spatial omics, which allows for profiling a range of biomolecules with high spatial resolution across the central dogma of molecular biology directly in the tissue context, not only offers spatial information but unlocks unprecedented new opportunities to delve into clinical specimens for human biology research, therapeutic discovery, and translational medicine. Spatial omics is becoming one of the fastest-paced growth areas in the biotech industry and poised to drive the next wave of biology revolution with widespread and far-reaching impact in all major fields of life science and medicine.GEN Biotechnology is pleased to announce a call for papers for our inaugural special issue—Spatial Omics.This collection of research articles, reviews, and perspectives will be published in late 2023. We invite researchers to submit without delay manuscripts describing original research on any aspect of spatial and single-cell biological research. We will also consider relevant guest commentaries and review articles.Specific topics may include (but are not confined to): Sequencing based spatial omics (i.e., transcriptome, proteome, epigenome, genome).High-plex imaging of proteins, transcripts, or epigenomic/genomic featuresSpatial proteomics and metabolomicsSpatial multi-omics and multi-modality tissue profilingComputational methods and tools for spatial biology (machine learning, data deconvolution, mathematical modeling, data visualization)Spatial omics to profile tumor heterogeneity and microenvironmentsSpatial omics in neuroscience, neurological or neurodegenerative disease researchSpatial omics in aging, senescence, metabolic and chronic diseases.Manuscripts will receive prompt peer review and accepted articles will be published online (epub) ahead of print. Please refer to our Instructions for Authors at www.liebertpub.com/genbio before submitting your manuscript.Presubmission inquiries may be sent to GEN Biotechnology (editor@genbiotechjournal.com). This special issue will be published in late 2023.Advantages of publishing in GEN Biotechnology include:Rapid, high-quality peer review, and editorial oversightFast electronic submissionMaximum exposure: accessible in 170 countries worldwideHigh visibility: International press and social media outreachOpen Access options availableVisit the Instructions for Authors:www.liebertpub.com/genbioSubmit your paper for peer review online:https://mc.manuscriptcentral.com/genbioFiguresReferencesRelatedDetails Volume 2Issue 2Apr 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Guest Editors: Rong Fan and Omer Bayraktar.Special Issue: Spatial Omics.GEN Biotechnology.Apr 2023.61-62.http://doi.org/10.1089/genbio.2023.29076.cfp2Published in Volume: 2 Issue 2: April 18, 2023PDF download

Jacques E. Dumont (July 19, 1931-February 6, 2023).

Jacques E. Dumont (July 19, 1931-February 6, 2023).

More than Ethics: Changing Approaches to Research in Human Biology

More than Ethics: Changing Approaches to Research in Human Biology

Integrative Proteomics and Phosphoproteomics Analysis of the Rat Adenohypophysis after GnRH Treatment

The regulation of mammalian reproductive activity is tightly dependent on the HPG axis crosstalk, in which several reproductive hormones play important roles. Among them, the physiological functions of gonadotropins are gradually being uncovered. However, the mechanisms by which GnRH regulates FSH synthesis and secretion still need to be more extensively and deeply explored. With the gradual completion of the human genome project, proteomes have become extremely important in the fields of human disease and biological process research. To explore the changes of protein and protein phosphorylation modifications in the adenohypophysis after GnRH stimulation, proteomics and phosphoproteomics analyses of rat adenohypophysis after GnRH treatment were performed by using TMT markers, HPLC classification, LC/MS, and bioinformatics analysis in this study. A total of 6762 proteins and 15,379 phosphorylation sites contained quantitative information. Twenty-eight upregulated proteins and fifty-three downregulated proteins were obtained in the rat adenohypophysis after GnRH treatment. The 323 upregulated phosphorylation sites and 677 downregulated phosphorylation sites found in the phosphoproteomics implied that a large number of phosphorylation modifications were regulated by GnRH and were involved in FSH synthesis and secretion. These data constitute a protein-protein phosphorylation map in the regulatory mechanism of "GnRH-FSH," which provides a basis for future studies on the complex molecular mechanisms of FSH synthesis and secretion. The results will be helpful for understanding the role of GnRH in the development and reproduction regulated by the pituitary proteome in mammals.

Special Issue: Spatial Omics

GEN BiotechnologyVol. 2, No. 1 Call for PapersFree AccessSpecial Issue: Spatial OmicsDeadline for Manuscript Submission: May 15, 2023Guest Editors: Rong Fan and Omer BayraktarGuest Editors: Rong FanYale UniversitySearch for more papers by this author and Omer BayraktarWellcome Sanger InstituteSearch for more papers by this authorPublished Online:15 Feb 2023https://doi.org/10.1089/genbio.2023.29076.cfpAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Single-cell omics has revolutionized biological and biomedical research in the past decade despite the inability to measure single cells in the tissue context. Spatial omics, which allows for profiling a range of biomolecules with high spatial resolution across the central dogma of molecular biology directly in the tissue context, not only offers spatial information but unlocks unprecedented new opportunities to delve into clinical specimens for human biology research, therapeutic discovery, and translational medicine. Spatial omics is becoming one of the fastest-paced growth areas in the biotech industry and poised to drive the next wave of biology revolution with widespread and far-reaching impact in all major fields of life science and medicine.GEN Biotechnology is pleased to announce a call for papers for our inaugural special issue—Spatial Omics.This collection of research articles, reviews, and perspectives will be published in late 2023. We invite researchers to submit without delay manuscripts describing original research on any aspect of spatial and single-cell biological research. We will also consider relevant guest commentaries and review articles.Specific topics may include (but are not confined to): Sequencing based spatial omics (i.e., transcriptome, proteome, epigenome, genome).High-plex imaging of proteins, transcripts, or epigenomic/genomic featuresSpatial proteomics and metabolomicsSpatial multi-omics and multi-modality tissue profilingComputational methods and tools for spatial biology (machine learning, data deconvolution, mathematical modeling, data visualization)Spatial omics to profile tumor heterogeneity and microenvironmentsSpatial omics in neuroscience, neurological or neurodegenerative disease researchSpatial omics in aging, senescence, metabolic and chronic diseases.Manuscripts will receive prompt peer review and accepted articles will be published online (epub) ahead of print. Please refer to our Instructions for Authors at www.liebertpub.com/genbio before submitting your manuscript.Presubmission inquiries may be sent to GEN Biotechnology (editor@genbiotechjournal.com). This special issue will be published in late 2023.Advantages of publishing in GEN Biotechnology include:Rapid, high-quality peer review, and editorial oversightFast electronic submissionMaximum exposure: accessible in 170 countries worldwideHigh visibility: International press and social media outreachOpen Access options availableVisit the Instructions for Authors:www.liebertpub.com/genbioSubmit your paper for peer review online:https://mc.manuscriptcentral.com/genbioFiguresReferencesRelatedDetails Volume 2Issue 1Feb 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Guest Editors: Rong Fan and Omer Bayraktar.Special Issue: Spatial Omics.GEN Biotechnology.Feb 2023.3-4.http://doi.org/10.1089/genbio.2023.29076.cfpPublished in Volume: 2 Issue 1: February 15, 2023PDF download

Human retina – A history of biological research and the development of genetic engineering

AbstractThe development of genetic engineering (also called genetic modification) started in the 40‐ties of the 19th c. After the Second World War the rapid process that used laboratory‐based technologies to conduct researches on cells, tissues, alter the DNA makeup of an organism and virus become the basis of modern paradigm of medical sciences. This was the culminating point of the process, which is sometimes called “the war against diseases”. One of the most successful moments was the creation of vaccines by combining genetic engineering research with research on viruses. It was a time of scientific optimism. For the first time in human history people could get the knowledge of aetiology of diseases, could fight them and protect themselves against infection. Its seems that the development of medical sciences could serve mankind, therefore there should be no limits as to its development. This optimism was not hindered by Nazists medical experimentations performed during the Second World War. However, The main ethical questions about the limits of medical science and human biological material research were left unanswered. The development of genetic engineering gave rise to questions on legalization of abortion, euthanasia, and transplantology. From 60‐ties to 90‐ties of the 20th century, large‐scale research began on diploid cells of fetal origin. All these events have called for discussion in the bioethics community and the question of the limits to which medical sciences can be pushed.Key word: history of genetic engineering, cell biology, history of human biological material research.

Minimally invasive biomarkers in human population biology research, part 2: An introduction to the special issue.

Over the past several decades, biomarkers have become indispensable tools in human biology, allowing researchers to investigate biocultural and evolutionary questions and to generate basic data on health and well-being. Human biologists are central players in biomarker methods development, pioneering the creation of "field friendly," minimally invasively collected biomarker approaches, as well as leading the innovative use of biomarkers, most notably to map the complex pathways from social and environmental conditions to altered physiology to health effects. This special issue, Part 2 of a collection focused on minimally invasively collected biomarkers, is comprised of nine papers that jointly contribute to driving the science of biomarker methods development and application. This compilation of papers engages with topics such as biological normalcy, ecoimmunology, and the ethics of working with vulnerable and underserved populations. It also focuses attention on research areas at present not emphasized in human biology such as bone turnover markers as a window onto osteoporosis and osteoarthritis and the use of cancer-related biomarkers in population screening and epidemiology. Taken together, these papers help draw the roadmap for future biomarker work, emphasizing: (1) the need for systematic and transparent approaches to assay validation, with open access publication; (2) simultaneous measurement of multiple biomarkers and expanded use of instrument platforms that increase the range of physiological, genomics, and omics markers available to researchers; and, (3) increased attention to ethics and researcher responsibilities, encouraging a mindset that recognizes our obligation to provide benefits to individuals and communities and to help redress past abuses.

Toolkit article: Approaches to measuring social inequities in health in human biology research.

Across populations, human morbidity and mortality risks generally follow clear gradients, with socially-disadvantaged individuals and groups tending to have higher morbidity and mortality at all life stages relative to those more socially advantaged. Anthropologists specialize in understanding the proximate and ultimate factors that shape variation in human biological functioning and health and are therefore well-situated to explore the relationships between social position and health in diverse ecological and cultural contexts. While human biologists have developed sophisticated methods for assessing health using minimally-invasive methods, at a disciplinary level, we have room for conceptual and methodological improvement in how we frame, measure, and analyze the social inequities that might shape health inequities. This toolkit paper elaborates on some steps human biologists should take to enhance the quality of our research on health inequities. Specifically, we address: (1) how to frame unequal health outcomes (i.e., inequalities vs. disparities vs. inequities) and the importance of identifying our conceptual models of how these inequities emerge; (2) how to measure various axes of social inequities across diverse cultural contexts, and (3) approaches to community collaboration and dissemination. We end by discussing (4) future directions in human biology research of health inequities, including understanding the ultimate causes of sensitivity to social inequities and transitioning from research to action.

Bringing the lab bench to the field: Point-of-care testing for enhancing health research and stakeholder engagement in rural/remote, indigenous, and resource-limited contexts.

Point-of-care testing (POCT) allows researchers and health-care providers to bring the lab bench to the field, providing essential health information that can be leveraged to improve health care, accessibility, and understanding across clinical and research settings. Gaps in health service access are most pronounced in what we term RIR settings-rural/remote regions, involving Indigenous peoples, and/or within resource-limited settings. In these contexts, morbidity and mortality from infectious and non-communicable diseases are disproportionately higher due to numerous geographic, economic, political, and sociohistorical factors. Human biologists and global health scholars are well-positioned to contribute on-the-ground-level insights that can serve to minimize global health inequities and POCT has the potential to augment such approaches. While the clinical benefits of POCT include increasing health service access by bringing testing, rapid diagnosis, and treatment to underserved communities with limited pathways to centralized laboratory testing, POCT also provides added benefits to both health-focused researchers and their participants. Through portable, minimally invasive devices, researchers can provide actionable health data to participants by coupling POCT with population-specific health education, discussing results and their implications, creating space for participants to voice concerns, and facilitating linkages to treatment. POCT can also strengthen human biology research by shedding light on questions of evolutionary and biocultural importance. Here, we expand on the epidemiological and research value, as well as practical and ethical challenges of POCT across stakeholders (i.e., participant, community, health researcher, and trainee). Finally, we emphasize the immense opportunities of POCT for fostering collaborative research and enhancing access to health delivery and information and, by extension, helping to mitigate persistent global health inequities.

Efficient targeted transgenesis of large donor DNA into multiple mouse genetic backgrounds using bacteriophage Bxb1 integrase

The development of mouse models of human disease and synthetic biology research by targeted transgenesis of large DNA constructs represent a significant genetic engineering hurdle. We developed an efficient, precise, single-copy integration of large transgenes directly into zygotes using multiple mouse genetic backgrounds. We used in vivo Bxb1 mediated recombinase-mediated cassette exchange (RMCE) with a transgene “landing pad” composed of dual heterologous Bxb1 attachment (att) sites in cis, within the Gt(ROSA)26Sor safe harbor locus. RMCE of donor was achieved by microinjection of vector DNA carrying cognate attachment sites flanking the donor transgene with Bxb1-integrase mRNA. This approach achieves perfect vector-free integration of donor constructs at efficiencies > 40% with up to ~ 43 kb transgenes. Coupled with a nanopore-based Cas9-targeted sequencing (nCATS), complete verification of precise insertion sequence was achieved. As a proof-of-concept we describe the development of C57BL/6J and NSG Krt18-ACE2 models for SARS-CoV2 research with verified heterozygous N1 animals within ~ 4 months. Additionally, we created a series of mice with diverse backgrounds carrying a single att site including FVB/NJ, PWK/PhJ, NOD/ShiLtJ, CAST/EiJ and DBA/2J allowing for rapid transgene insertion. Combined, this system enables predictable, rapid development with simplified characterization of precisely targeted transgenic animals across multiple genetic backgrounds.

Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.

Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier.

Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.