Miracle-dz/UniFAR-FTUs huggingface dataset:
“Dual protease type XIII/pepsin digestion offers superior resolution and overlap for the analysis of histone tails by HX-MS”

The N-terminal regions of histone proteins (tails) are dynamic elements that protrude from the nucleosome and are involved in many aspects of chromatin organization. Their epigenetic role is well-established, and post-translational modifications (PTMs) present on these regions contribute to transcriptional regulation. While hydrogen/deuterium exchange mass spectrometry (HX-MS) is well-suited for the analysis of dynamic structures, it has seldom been employed to analyze histones due to the poor N-terminal coverage obtained using pepsin. Here, we test the applicability of a dual protease type XIII/pepsin digestion column to this class of proteins. We optimize online digestion conditions using the H4 monomer, and extend the method to the analysis of histones in monomeric states and nucleosome core particles (NCPs). We show that the dual protease column generates many short and overlapping N-terminal peptides. We evaluate our method by performing hydrogen exchange experiments of NCPs for different time points and present full coverage of the tails at excellent resolution. We further employ electron transfer dissociation (ETD) and showcase an unprecedented degree of overlap across multiple peptides that is several fold higher than previously reported methods. The method we report here may be readily applied to the HX-MS investigation of histone dynamics and to the footprints of histone binding proteins on nucleosomes.
New concept of physiologic anchorage control

Molar anchorage loss in extraction case is believed due to the reaction of mechanical force applied to retract anterior teeth. While it may be close to truth in adult patients, it is certainly not true in adolescents. Studies on molar growth show upper molar move forward as mandible growing forward, probably through intercuspation force. Hence, for adolescents, molar anchorage loss shall consist of two parts. One is from retraction force - mechanical anchorage loss; another from biologic force - physiologic anchorage loss. Since physiologic anchorage loss is caused by the continuous biologic force, the strategy of physiologic anchorage control (PAC) is different from the strategy of mechanical anchorage control. A new PAC method is introduced in this article that can reduce the headgear and temporary anchorage device used as sagittal anchorage dramatically in orthodontic clinic.
Genetic And Epigenetic Regulation Of E-Cadherin Signaling In Human Hepatocellular Carcinoma

Abstract E-cadherin is well known as a growth and invasion suppressor and belongs to the large cadherin family. Loss of E-cadherin is widely known as the hallmark of epithelial-to-mesenchymal transition (EMT) with the involvement of transcription factors such as Snail, Slug, Twist and Zeb1/2. Tumor cells undergoing EMT could migrate to distant sites and become metastases. Recently, numerous studies have revealed how the expression of E-cadherin is regulated by different kinds of genetic and epigenetic alteration, which are implicated in several crucial transcription factors and pathways. E-cadherin signaling plays an important role in hepatocellular carcinoma (HCC) initiation and progression considering the highly mutated frequency of CTNNB1 (27%). Combining the data from The Cancer Genome Atlas (TCGA) database and previous studies, we have summarized the roles of gene mutations, chromosome instability, DNA methylation, histone modifications and non-coding RNA in E-cadherin in HCC. In this review, we discuss the current understanding of the relationship between these modifications and HCC. Perspectives on E-cadherin-related research in HCC are provided.
A novel method to detect intracellular metabolite alterations in MCF-7 cells by doxorubicin induced cell death

Metabolic reprogramming within cancer cells is suggested as a potential barrier to chemotherapy. Additionally, metabolic tumor heterogeneity is one of factor behind discernible hallmarks such as drug resistance, relapse of tumor and the formation of secondary tumors. In this paper, cell based assays including PI/annexin V staining and immunoblot assay were performed to show the apoptotic cell death in MCF-7 cells treated with DOX. Further, MCF-7 cells were lysed in hypotonic buffer and whole cell lysate was purified by a novel and specifically designed metabolite (100 to 1000 Da) fractionation system as vertical tube gel electrophoresis (VTGE). Further, purified intracellular metabolites were subjected to identification by LC-HRMS technique. The authors show the presence of cleaved PARP 1 in MCF-7 cells treated with DOX. Concomitantly, data show the absence of active caspase 3 in MCF-7 cells. Novel findings are to identify key intracellular metabolites assisted by VTGE system that include lipid (CDP-DG, phytosphingosine, dodecanamide), non-lipid (N-acetyl-D-glucosamine, N1-acetylspermidine and gamma-L-glutamyl-L-cysteine) and tripeptide metabolites in MCF-7 cells treated by DOX. Interestingly, the authors report a first evidence of doxorubicinone, an aglycone form of DOX in MCF-7 cells that is potentially linked to the mechanism of cell death in MCF-7 cells. This paper reports on novel methods and processes that involve VTGE system based purification of hypotonically lysed novel intracellular metabolites of MCF-7 cells treated by DOX. Here, these identified intracellular metabolites corroborate to caspase 3 independent and mitochondria induced apoptotic cell death in MCF-7 cells. SIGNIFICANCE STATEMENT Metabolic reprogramming in cancer cells is implicated in various tumor hallmarks. Interestingly, thousands of research have addressed the molecular basis of drug treatment and resistance in chemotherapy. But, there is a significant gap in the precise methodologies and approaches in addressing intracellular metabolite alterations. This paper reports on a novel approach that helped reveal new findings on intracellular metabolite changes in case of doxorubicin (DOX) induced cell death in MCF-7 cells. This paper highlights the additional insights on debatable findings available in literature in the contexts of DOX induced cell death mechanisms. In this paper, novel and specifically designed vertical tube gel electrophoresis (VTGE) system is claimed to purify intracellular metabolites and this method is compatible with other biological system.
The Golgi Glycoprotein MGAT4D Protects Testicular Germ Cells From Mild Heat Stress

MGAT4D was identified as an inhibitor of MGAT1 in the Golgi of transfected cells. MGAT1 is the GlcNAc-transferase that initiates complex and hybrid N-glycan synthesis in mammals. Conditional deletion of Mgat1 in spermatogonia leads to a block in spermatogenesis and infertility in mice. Mgat4d is highly expressed in spermatocytes and spermatids. Here we show that, unexpectedly, when the Mgat4d gene was inactivated globally or conditionally in spermatogonia, or mis-expressed in spermatogonia, spermatocytes or spermatids, neither spermatogenesis nor fertility were affected. MGAT1 activity was also not inhibited in germ cells. On the other hand, when males were subjected to mild heat stress of the testis (43°C for 25 min), a novel function for MGAT4D was revealed. Germ cells with inactivated Mgat4d were markedly more sensitive to the effects of mild heat stress, and transgenic mice expressing Mgat4d in spermatogonia, spermatocytes or spermatids were partially protected from heat stress. Microarray data from germ cells of heat-stressed mutant versus control males showed that germ cells lacking Mgat4d generally mounted a similar heat shock response to control germ cells, but could not maintain that response. Several pathways and genes activated by heat stress in wild type were induced to a lesser extent in Mgat4d[-/-] heat-stressed germ cells, including the NFκB response, pro-inflammatory pathways such as TNF and TGFβ signaling, and genes that promote proliferation such as Hif1α and Myc. Thus, MGAT4D protects male germ cells from the deleterious consequences of heat stress.
Caenorhabditis elegans AF4/FMR2 family homolog affl-2 is required for heat shock induced gene expression

To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat shock induced gene expression in C. elegans, we identified a new allele of hsf-1 that alters its DNA-binding domain, and three additional alleles of sup-45, a previously uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). affl-2 mutants are egg-laying defective and dumpy, but worms lacking its sole paralog (affl-1) appear wild-type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream or parallel of hsf-1. Our characterization of affl-2 provides insights into the complex processes of transcriptional elongation and regulating heat shock induced gene expression to protect against heat stress.
Enhancements to U.S. genetic and genomic evaluations in 2018 and 2019

In 2013, the Council on Dairy Cattle Breeding (CDCB) started calculating and releasing U.S. genetic and genomic evaluations, which historically had been totally managed by USDA. The role of USDA in the U.S. dairy genetics industry is still extremely important because USDA’s Animal Genomic and Improvement Laboratory conducts most of the research for developing the cutting-edge methodologies applied by CDCB. This presentation reviews the latest enhancements to U.S. evaluations during 2018 and 2019, all of them result of the interaction between public service and private U.S. industry. In April 2018, CDCB introduced six new health traits for Holsteins; these traits were included in lifetime net merit in August 2018. Early first calving, another new trait, was introduced in April 2019. In April 2018, CDCB also extended genomic evaluation to an all-breed system, which had been used for traditional evaluations since 2007. This, together with further methodology developments to determine an animal’s breed composition (breed base representation, or BBR), resulted in the first release of a multi-breed genomic evaluation for crossbred animals in April 2019. In December 2018, the reference genome assembly was updated from the UMD3 version to the latest ARS-UCD1 version. At the same time, the number of markers used in genomic evaluations was increased from 60k to 80k. The new set of markers included more exact gene tests, removed poorer performers, added new variants with larger effects on traits, and changed the marker order based on the new assembly. The latest discovered recessive haplotype in Holsteins (HH6, BTAU-16) also was released in December 2018, and haplotypes BH1 (Brown Swiss) and JH2 (Jersey) were discontinued. Further enhancements were applied to productive life and fertility traits in 2018. Future projects include the release of evaluations for Jersey health traits, further improvements to the marker set, and enhancements of crossbred evaluation.
Linking and characterizing biologic scales of imaging data: applications to prostate cancer diagnosis

OF THE DISSERTATION Linking and Characterizing Biologic Scales of Imaging Data: Applications to Prostate Cancer Diagnosis by Rachel Sparks Dissertation Director: Anant Madabhushi Prostate cancer is the second most commonly diagnosed cancer of men, an estimated 192,000 men are diagnosed each year in the United States (source: American Cancer Society). The current gold standard for prostate cancer diagnosis is pathologist inspection of prostate needle biopsy samples obtained using transrectal ultrasound (TRUS). TRUS-guided biopsy is routine because TRUS is widely available and acquires real-time imagery. However, TRUS-guided biopsy has a low sensitivity, and initial biopsy misses approximately half of all men with prostate cancer. Multi-parametric Magnetic Resonance Imaging (MRI) has shown promise in detecting, localizing, and grading prostate cancer. MRI-TRUS fusion, whereby MRI is acquired pre-operatively then aligned to TRUS during biopsy, allows for both modalities to be leveraged. MRI-TRUS fusion will enable the construction of joint classifiers, which leverage imaging characteristics on both MRI and TRUS, to detect, localize, and grade prostate cancer. In order to train and validate these classifiers, ground truth spatial extent and aggressiveness of prostate cancer must be obtained. Manual pathologist inspection provides the ultimate definitive diagnosis of prostate cancer, with the Gleason grading system providing a measure of prostate cancer aggressiveness. Therefore whole mount histopathology (WMH) is aligned to fused MRI-TRUS imagery to provide ground truth of cancer location and
The tetraspanin Tspan15 is an essential subunit of an ADAM10 scissor complex

A disintegrin and metalloprotease 10 (ADAM10) is a transmembrane protein essential for embryonic development, and its dysregulation underlies disorders such as cancer, Alzheimer's disease, and inflammation. ADAM10 is a “molecular scissor” that proteolytically cleaves the extracellular region from >100 substrates, including Notch, amyloid precursor protein, cadherins, growth factors, and chemokines. ADAM10 has been recently proposed to function as six distinct scissors with different substrates, depending on its association with one of six regulatory tetraspanins, termed TspanC8s. However, it remains unclear to what degree ADAM10 function critically depends on a TspanC8 partner, and a lack of monoclonal antibodies specific for most TspanC8s has hindered investigation of this question. To address this knowledge gap, here we designed an immunogen to generate the first monoclonal antibodies targeting Tspan15, a model TspanC8. The immunogen was created in an ADAM10-knockout mouse cell line stably overexpressing human Tspan15, because we hypothesized that expression in this cell line would expose epitopes that are normally blocked by ADAM10. Following immunization of mice, this immunogen strategy generated four Tspan15 antibodies. Using these antibodies, we show that endogenous Tspan15 and ADAM10 co-localize on the cell surface, that ADAM10 is the principal Tspan15-interacting protein, that endogenous Tspan15 expression requires ADAM10 in cell lines and primary cells, and that a synthetic ADAM10/Tspan15 fusion protein is a functional scissor. Furthermore, two of the four antibodies impaired ADAM10/Tspan15 activity. These findings suggest that Tspan15 directly interacts with ADAM10 in a functional scissor complex.
Beyond DNA sequence: Exploring and Exploiting Mammalian DNA Methylation

Author(s): He, Yupeng | Advisor(s): Ecker, Joseph R | Abstract: Cytosine DNA methylation (mC) is a chemical modification prevalent in mammalian genome and it plays important roles in transcriptional regulation, development and cell differentiation. Recent studies reveal that mC affects how DNA is interpreted, like an additional information layer on top of the genetic code. Results of both in vitro and in vivo experiments demonstrate that mC is influential on the binding affinity of a number of transcription factors. Furthermore, targeted addition/removal of mC was shown to modulate gene transcription. In addition, while mC was thought to be a stable chemical decoration on DNA, it can be dynamically added or removed during biological processes such as cell differentiation, and its distribution is distinct in different cell types and tissues. Given mC's potential functional impact and cell/tissue specificity, systematically profiling mC across a variety of cell types and tissues is essential for understanding its biological significance. To fill this gap, I first worked with colleagues to dissect the mC landscape of 18 human tissue types from 4 individual. We systematically compared the mC distribution in these human tissues and identified over a million differentially methylated regions, which are strongly overlapped with tissue-specific regulatory DNA elements. The dataset serves as the mC state baseline of normal human tissues. In my second thesis project, I exploited the mC information and developed a computational approach called REPTILE to improve the identification of enhancers, the regulatory DNA elements that promote the transcription of their target genes. Finally, I worked with colleagues to investigate the temporal mC regulation in 12 developing mouse fetal tissues. Our results indicate that mC changes dramatically during development primarily at regulatory DNA elements and it shows a trend of demethylation at fetal stages followed by remethylation after birth. I applied REPTILE on this dataset and delineated hundreds of thousands of transcriptional regulatory DNA elements that are related to tissue development.
Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks

Reuse of standing genetic variation is thought to be the main mechanism behind the repeated evolution of the same phenotypes in similar environments. An important model system for the study of genomic mechanisms underlying parallel ecological adaptation in the wild is the three-spined stickleback (Gasterosteus aculeatus), which has repeatedly colonized and adapted to freshwater from the sea. Previous studies have identified numerous genomic regions showing consistent genetic divergence between freshwater and marine ecotypes, but most of these studies have been based on limited geographic sampling, and with strong biases towards studies conducted in the Eastern Pacific area. We analysed population genomic data from three-spined sticklebacks with comprehensive global sampling using unsupervised methods to detect loci involved in parallel evolution at different geographical areas. In line with previous studies, we find several genomic regions, including two chromosomal inversions, contributing to global differentiation of marine and freshwater ecotypes. However, signatures of parallel evolution were far stronger in the Eastern Pacific region than anywhere else in the world. With simulations, we demonstrate that since freshwater-adapted alleles exist in the marine populations only at low frequencies, they are easily lost during founder events, thereby reducing the amount of standing genetic variation available for freshwater adaptation outside of the ancestral Eastern Pacific region. Hence, geographic heterogeneity in access to standing genetic variation due to historical demographic factors appears to provide an explanation to marked geographic differences in the pervasiveness of parallel evolution in the three-spined stickleback. Therefore, the degree of genetic parallelism in the three-spined stickleback model system appears not be as pervasive as earlier studies focused on Eastern Pacific populations have led us to believe.
ChpC controls twitching motility-mediated expansion of Pseudomonas aeruginosa biofilms in response to serum albumin, mucin and oligopeptides

Twitching motility-mediated biofilm expansion occurs via coordinated, multi-cellular collective behaviour to allow bacteria to actively expand across surfaces. Type-IV pili (T4P) are cell-associated virulence factors which mediate this expansion via rounds of extension, surface attachment and retraction. The Chp chemosensory system is thought to respond to environmental signals to regulate the biogenesis, assembly and twitching motility function of T4P. In other well characterised chemosensory systems, methyl-accepting chemotaxis proteins (MCPs) feed environmental signals through a CheW adapter protein to the histidine kinase CheA to modulate motility. The Pseudomonas aeruginosa Chp system has two CheW adapter proteins, PilI and ChpC, and an MCP PilJ that likely interacts via PilI with the histidine kinase ChpA. It is thought that ChpC associates with other MCPs to feed environmental signals into the system, however no such signals have been identified. In the current study we show that ChpC is involved in the response to host-derived signals serum albumin, mucin and oligopeptides. We demonstrate that these signals stimulate an increase in twitching motility, as well as in levels of 3’-5’-cyclic adenosine monophosphate (cAMP) and surface-assembled T4P. Interestingly, our data shows that changes in cAMP and surface piliation levels are independent of ChpC but that the twitching motility response to these environmental signals requires ChpC. Based upon our data we propose a model whereby ChpC associates with an MCP other than PilJ to feed these environmental signals through the Chp system to control twitching motility. The MCP PilJ and the CheW adapter PilI then modulate T4P surface levels to allow the cell to continue to undergo twitching motility. Our study is the first to link environmental signals to the Chp chemosensory system and refines our understanding of how this system controls twitching motility-mediated biofilm expansion in P. aeruginosa.
An Emerging Middle Range Theory for Global Nursing Practice in Communities of Faith

Chronic illness poses a challenge for traditional global health care models. Health care systems in countries of varying sizes and resources are all struggling to develop efficient care delivery models responsive to communities and individuals. Persons and families living with chronic illness desire not only symptom management but also whole-person approaches that address coping strategies for emotional, physical and spiritual needs.
An Optimal Integrated Vector Control for Prevention the Transmission of Dengue

Dengue is a tropical infectious disease caused by dengue virus which is transmitted by mosquitos such as Aedes Aegypti and Aedes Albopictus. The spread of this disease could be controlled by applying some optimal strategies. In this research, we study optimal strategy in controlling the spread of dengue by taking into consideration an integrated vector control strategy. The strategy combines chemical and non-chemical vector control methods to prevent the transmission of vector-borne disease. If we assume that the control functions are constant functions then numerically we obtain a critical chemical control which leads to the non-endemic condition. When the chemical and non-chemical controls are varying in time, we obtain the analytical form of the both control functions by using Pontryagin Maximum Principle. The numerical simulations are performed using the Steepest Descent method and the results show that the peak of the non-chemical control effect occurs at the end of the observation time. Conversely, the chemical control reaches the maximum effect at the early of the observation time. It indicates that the integrated vector control strategy is a continuous prevention method that succefully ensures the system free from dengue infection.