Life Sciences Commons^™

Metagenomics Reveals The Temporal Dynamics Of The Rumen Resistome And Microbiome In Goat Kids, Jianmin Chai, Yimin Zhuang, Kai Cui, Yanglin Zhu, Yangliang Bi, Naifeng Zhang

Animal Science Faculty Publications and Presentations

Background

The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early …

Willingness-To-Pay For Rationed Goods: Bobcat Harvest Permits In Indiana, Nicholas A. Lancaster, Carson Reeling, John G. Lee, Richard T. Melstrom, Joe N. Caudell, Geriann Albers

Department of Agricultural Economics Faculty Publications

We use contingent valuation to estimate hunter and trapper willingness to pay (WTP) for a hypothetical bobcat harvest permit being considered in Indiana. Harvest permits would be rationed, with limits on aggregate and individual harvests. A model of permit demand shows that WTP may be subject to “congestion effects” which attenuate welfare gains from relaxing harvest limits. Intuitively, relaxing limits may directly change an individual’s expected harvest and, hence, WTP. Participation may subsequently change, with congestion offsetting welfare increases. These effects may lead to apparent scope insensitivity that may be endemic in the context of rationed goods.

Interplay Between Acetylation And Ubiquitination Of Imitation Switch Chromatin Remodeler Isw1 Confers Multidrug Resistance In Cryptococcus Neoformans, Yang Meng, Yue Ni, Zhuoran Li, Tianhang Jiang, Tianshu Sun, Yanjian Li, Xindi Gao, Hailong Li, Chenhao Suo, Chao Li, Sheng Yang, Tian Lan, Guojian Liao, Tongbao Liu, Ping Wang, Chen Ding

School of Medicine Faculty Publications

Cryptococcus neoformans poses a threat to human health, but anticryptococcal therapy is hampered by the emergence of drug resistance, whose underlying mechanisms remain poorly understood. Herein, we discovered that Isw1, an imitation switch chromatin remodeling ATPase, functions as a master modulator of genes responsible for in vivo and in vitro multidrug resistance in C. neoformans. Cells with the disrupted ISW1 gene exhibited profound resistance to multiple antifungal drugs. Mass spectrometry analysis revealed that Isw1 is both acetylated and ubiquitinated, suggesting that an interplay between these two modification events exists to govern Isw1 function. Mutagenesis studies of acetylation and ubiquitination sites …

Fusionnw, A Potential Clinical Impact Assessment Of Kinases In Pan-Cancer Fusion Gene Network

Faculty, Staff and Student Publications

Kinase fusion genes are the most active fusion gene group in human cancer fusion genes. To help choose the clinically significant kinase so that the cancer patients that have fusion genes can be better diagnosed, we need a metric to infer the assessment of kinases in pan-cancer fusion genes rather than relying on the sample frequency expressed fusion genes. Most of all, multiple studies assessed human kinases as the drug targets using multiple types of genomic and clinical information, but none used the kinase fusion genes in their study. The assessment studies of kinase without kinase fusion gene events can …

Unexpected Inhibition Of The Lipid Kinase Pikfyve Reveals An Epistatic Role For P38 Mapks In Endolysosomal Fission And Volume Control, Daric J Wible, Zalak Parikh, Eun Jeong Cho, Miao-Der Chen, Collene R Jeter, Kevin N Dalby, Shawn B Bratton

Faculty, Staff and Student Publications

p38 mitogen-activated protein kinases (MAPKs) participate in autophagic signaling; and previous reports suggest that pyridinyl imidazole p38 MAPK inhibitors, including SB203580 and SB202190, induce cell death in some cancer cell-types through unrestrained autophagy. Subsequent studies, however, have suggested that the associated cytoplasmic vacuolation resulted from off-target inhibition of an unidentified enzyme. Herein, we report that SB203580-induced vacuolation is rapid, reversible, and relies on the class III phosphatidylinositol 3-kinase (PIK3C3) complex and the production of phosphatidylinositol 3-phosphate [PI(3)P] but not on autophagy per se. Rather, vacuolation resulted from the accumulation of Rab7 on late endosome and lysosome (LEL) membranes, combined with …

Acute Ingestion Of Dark Chocolate Fails To Affect Running Economy In Recreational Female Runners, Bianca J. De Lucia, Beau Kjerulf Greer, Christopher B. Taber

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 5: Issue 1, Article 1, 2024. Ingestion of dark chocolate (DC), a dietary source high in flavanols, may increase nitric oxide bioavailability. Elevating blood nitric oxide concentrations may augment metabolic efficiency by reducing the amount of oxygen or energy needed to perform a given task. Utilizing a crossover design, the purpose of this study was to investigate the effect of acute ingestion of DC on running economy (RE). Nineteen recreationally trained females (age: 20±1 years) volunteered for this investigation, with 16 completing all procedures (n = 16). Two-hours before RE assessment, participants consumed …

The Cetacean Sanctuary: A Sea Of Unknowns, Jason N. Bruck

Faculty Publications

Housing cetaceans in netted sea pens is not new and is common for many accredited managed- care facilities. Hence, the distinction between sanctuary and sea pen is more about the philosophies of those who run these sanctuary facilities, the effects of these philosophies on the animals’ welfare, and how proponents of these sanctuaries fund the care of these animals. Here, I consider what plans exist for cetacean sanctuaries and discuss the caveats and challenges associated with this form of activist-managed captivity. One goal for stakeholders should be to disregard the emotional connotations of the word “sanctuary” …

Current Status And Applications Of Microbial Chassis Strains For Chinese Biomanufacturing Industry, Guoqiang Chen, Fuqing Wu, Shuang Zheng, Jun Ding, Junting Sheng

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biomanufacturing is an important component of new quality productive forces, representing the commanding height of the new round of technological revolution and serving as a new engine for industrial transformation following information technology. It demonstrates vast application prospects in fields such as renewable energy, advanced materials, biomedicine, green food, and environmental protection. Biomanufacturing utilizes chassis microorganisms similar as “microchip” to produce various bioproducts via processes including chassis design and construction, large-scale cell cultivation, and product purifications. Most chassis microorganisms in biomanufacturing were not domestically identified. This study summarizes the types of common chassis microorganisms both domestically and internationally, as well …

Recent Progress And Perspectives On Development Of Gene Editing Tools, Zixian Liu, Chengping Li, Gogo Jun-Jie Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The gene editing field has witnessed remarkable advancements in recent years, leading to the establishment and refinement of multidimensional gene editing platforms. These innovations have enabled precise targeted gene knockout, repair, and insertion. These tools have stimulated significant progress in fundamental research, therapeutics, agriculture, environment protection, and industrial applications. In this review, we provide a comprehensive overview of the milestones in gene editing tool development and offer perspectives on potential future directions for this rapidly evolving field.

Digitalized Design Of Cell Factory Enables Green Biomanufacturing, Fanze Meng, Rui Cao, Bing Hu, Lei Qin, Chun Li

Bulletin of Chinese Academy of Sciences (Chinese Version)

Green manufacturing is a modern manufacturing mode in the consideration of both environmental impact and efficiency of resource utilization, it represents a significant component of the “new productive force”. Centered on cell factories, green biomanufacturing leverages renewable resources to efficiently produce products that conform to the concepts of low-carbon, green, and sustainable development. The design of high-performance cell factories is pivotal for achieving efficient green biomanufacturing. Nevertheless, traditional cell factory design processes are complex, time-consuming, and labor-intensive. With advancements in artificial intelligence, digital-assisted cell factory design has emerged as a solution to save time and reduce costs. By integrating technologies …

Research Progress In High-Throughput Phenotype Testing Technology And Equipment For Engineering Cells Based On Microfluidics, Shuang Li, Xiaojie Guo, Haibo Chen, Sisi Chen, Xin Da, Zhenghui Li, Qinxiu Liu, Yi Wang, Xinhui Xing, Chong Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Engineering cells are a core component of green bio-manufacturing. The efficient testing and acquisition of engineering cells with the desired phenotype is a critical factor in the successful implementation of bio-manufacturing. In recent years, based on microfluidics technologies, non-culture type single-cell phenotype high-throughput test equipment and culture type phenotype high-throughput test equipment for the growth and metabolism of single cell in a bioreactor have been developed such as microdroplet and microchamber, realizing high-throughput, automated, miniaturized, and integrated testing of the phenotypes of engineering cells and providing a powerful tool for the breeding of engineering cells. This review systematically compiles the …

Bioprocess Engineering And Intelligent Biomanufacturing, Guan Wang, Yingping Zhuang

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the era of rapid development of synthetic biology, biomanufacturing, as a bridge between life sciences and engineering technologies, is gradually demonstrating its extraordinary potential to reshape industrial landscapes. However, challenges such as production efficiency, cost control, and process monitoring still hinder the smooth transition from laboratory innovations to industrial-scale implementation. Intelligent biomanufacturing has emerged as a new form of productive force, offering innovative solutions to these problems. This study reviews the latest advances in bioprocess engineering and intelligent biomanufacturing, focusing on three key technological systems: intelligent sensing, intelligent analysis, and intelligent control. Intelligent sensing technology acts as the “eyes” …

Nine-Step Approach Of Smart Agricultural Helps Grain Production Reduce Costs, Increase Yield And Efficiency, Shuqin Gao, Zhaomin Hu, Hongsheng Wang, Xiaobo Zhang, Yucheng Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Food security is a top priority in national governance. Since 1949, high-standard farmland construction, agricultural mechanization development, and agricultural technology promotion have all contributed to the grain production. To ensure grain security, China has drawn a “red line” of 1.8 billion mu (about 120 million hectares) as the official minimum of arable land. At the same time, increasing the investment of capital goods such as fertilizer and pesticides can no longer produce more food. Due to the extensive farming method in the past, the continuous increase in total grain output becomes difficult in the future. With the rapid development of …

A New Paradigm Of Life Science Research Driven By Artificial Intelligence, Xin Li, Hanchao Yu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The rapid development of biotechnology and information technology has brought life sciences into a new era of data explosion. The traditional life science research paradigm struggles to reveal the fundamental rules of complex biological systems from rapidly growing biological big data. As artificial intelligence continues to achieve disruptive breakthroughs in life science, a new paradigm driven by AI is emerging. This study delves into typical examples of life science research driven by AI, proposes the concept and key elements of the new life science research paradigm, elaborates on the cutting-edge of life science research under this new paradigm, and discusses …

Technological Bottlenecks And Innovative Developments For Rubber Tree Breeding In China, Yongshuai Sun, Weimin Tian, Deli Zhai, Yongping Yang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Superior varieties of rubber trees are crucial elements in achieving stable production and supply of natural rubber. In China, rubber tree planting areas are situated at the northern edga of the world’s tropical zone and thus belong to non-traditional rubber tree planting areas with climatic conditions inferior to the traditional ones in Southeast Asia. The planted rubber trees are frequently damaged by low temperatures and diseases. Therefore, an urgent need in natural rubber production is to develop varieties with highyield potential and strong stress-tolerance. The scarcity of such varieties is mainly ascribed to the highly heterozygous genome, a long juvenile …

Microbial Production Of Feed Amino Acids Promotes Reduction And Replacement Of Soybean Meal, Jia Liu, Qi Sheng, Kaifang Liu, Liming Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

With the promotion of soybean meal reduction and substitution as well as lower-protein diet technologies, China has become a leading global producer of feed amino acids. However, the amino acid industry faces significant challenges due to its relatively late start in independently developing industrial strains, resulting in relatively lagging key economic and technical parameters and a less robust intellectual property framework. The rapid progress of synthetic biology has provided promising avenues for the design and optimization of industrial amino acid-producing strains, offering new opportunities for the amino acid fermentation industry to enhance the global competitiveness. This study offers an in-depth …

Current Status And Prospect Of Industrial Filamentous Fungi In Biomanufacturing, Zhiqiang Du, Ping Men, Yu Zhou, Xuan Zhang, Xuenian Huang, Xuefeng Lyu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Filamentous fungi, a critical class of industrial microorganisms pivotal to the biomanufacturing industry, has extensive applications in various fields such as pharmaceuticals, food, agriculture, and chemical materials, which are playing a vital role in human life. Recently, innovations in synthetic biology have further driven the application of industrial filamentous fungi in biomanufacturing, highlighting their critical role in this field. This article presents a comprehensive review of the recent progress in the field, covering the latest developments in genetic modification techniques for industrial filamentous fungi, successful cases of rational strain improvement strategies aimed to enhance the quality and efficiency of current …

Research On Innovative Development Path And Policy Guarantee Of China’S Synthetic Biology Industry, Hongjun Geng, Chang Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Synthetic biology is hailed as the third revolution in life sciences after the discovery of the DNA double helix structure and genomic technology, and is the core driving force for the leapfrog development of next-generation biomanufacturing and the future bioeconomy, opening up an opportunity window for the reshaping of the global manufacturing map. How to strategically position the synthesis biology industry and seize the strategic high ground in the industry is a core topic of interest for global science and technology powers and manufacturing powers. Based on the identification of problems in the development of China’s synthesis biology industry, this …

Internal Logic And Policy Recommendations Of Big Data To Support High-Quality Development Of Modern Agricultural Industry, Yingming Li, Zitong Wang, Mingyue Wang, Shiyi Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Clarifying the internal logic of big data to support modern agricultural production is helpful to cultivate and develop new quality productive forces in agriculture. From the perspective of economics, this study proposes that the role of big data in modern agricultural production is mainly reflected in two levels. Firstly, it improves the total factor productivity of the traditional agricultural production function. Secondly, it changes the factor endowment structure of agricultural production and forms a new agricultural production function. Based on these, the realization form of big data to support modern agricultural production can be summarized as improving the efficiency of …

Redesign And De Novo Design Of Circular Blue Bioindustry, Wei Zhang, Shufeng Zhang, Hantao Zhou, Minhan Dai

Bulletin of Chinese Academy of Sciences (Chinese Version)

The future marine bioindustry, which features advanced green intelligent biomanufacturing and high-value marine bioproducts, is a strategically emerging marine industry. This study proposes a new industrial development model for the circular blue bioindustry, founded on simultaneously optimizing the sustainable utilization of marine bioresources and protecting the ecological environment. Through in-depth analysis of the current situation, challenges, and potential development opportunities of the global and Chinese marine bioindustries underpinning sustainable development, theoretical framework, approaches and implementation pathways have been established to redesign the existing marine bioindustry and de novo design of the emerging marine bioindustry. Future key development priorities are suggested …

Analysis On Development Status And Characteristics Of Non-Governmental Bio-Safety And Bio-Security Think Tanks In The United States, Wenbing Ma, Qiang Song, Lei Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

At present, the complexity of bio-safety governance is becoming increasingly prominent, and complex issues such as security and development in the bio-economy, preparedness and response to infectious disease pandemics, the interweaving and integration of bio-security and other security factors, and the integration of scientific and technological factors and security factors urgently require think tanks to conduct systematic, comprehensive and forward-looking assessments and provide professional solutions. Rooted in the relatively mature experience in the construction of think tanks in the United States, a number of bio-safety and bio-security think tanks with greater influence have been developed, which have acted as an …

Mypathway Human Epidermal Growth Factor Receptor 2 Basket Study: Pertuzumab + Trastuzumab Treatment Of A Tissue-Agnostic Cohort Of Patients With Human Epidermal Growth Factor Receptor 2-Altered Advanced Solid Tumors, Christopher J Sweeney, John D Hainsworth, Ron Bose, Howard A Burris, Razelle Kurzrock, Claire F Friedman, Tania Szado, Katja Schulze, Richard Price, Julia Malato, Amy A Lo, Jonathan Levy, Yong Wang, Wei Yu, Funda Meric-Bernstam

Faculty, Staff and Student Publications

Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.The MyPathway multiple-basket study (ClinicalTrials.gov identifier: NCT02091141) is evaluating targeted therapies in nonindicated tumors with relevant molecular alterations. We assessed pertuzumab + trastuzumab in a tissue-agnostic cohort of adult patients with human epidermal growth factor receptor …

Durvalumab Plus Carboplatin/Paclitaxel Followed By Maintenance Durvalumab With Or Without Olaparib As First-Line Treatment For Advanced Endometrial Cancer: The Phase Iii Duo-E Trial, Shannon N Westin, Kathleen Moore, Hye Sook Chon, Jung-Yun Lee, Jessica Thomes Pepin, Ayelet Shai, Shin Nishio, Michael A Gold, Ke Wang, Kristi Mcintyre, Todd D Tillmanns, Stephanie V Blank, Ji-Hong Liu, Michael Mccollum, Fernando Contreras Mejia, Tadaaki Nishikawa, Kathryn Pennington, Zoltan Novak, Andreia Cristina De Melo, Jalid Sehouli, Dagmara Klasa-Mazurkiewicz, Christos Papadimitriou, Marta Gil-Martin, Birute Brasiuniene, Conor Donnelly, Paula Michelle Del Rosario, Xiaochun Liu, Els Van Nieuwenhuysen, Duo-E Investigators

Faculty, Staff and Student Publications

PURPOSE: Immunotherapy and chemotherapy combinations have shown activity in endometrial cancer, with greater benefit in mismatch repair (MMR)-deficient (dMMR) than MMR-proficient (pMMR) disease. Adding a poly(ADP-ribose) polymerase inhibitor may improve outcomes, especially in pMMR disease.

METHODS: This phase III, global, double-blind, placebo-controlled trial randomly assigned eligible patients with newly diagnosed advanced or recurrent endometrial cancer 1:1:1 to: carboplatin/paclitaxel plus durvalumab placebo followed by placebo maintenance (control arm); carboplatin/paclitaxel plus durvalumab followed by maintenance durvalumab plus olaparib placebo (durvalumab arm); or carboplatin/paclitaxel plus durvalumab followed by maintenance durvalumab plus olaparib (durvalumab + olaparib arm). The primary end points were progression-free survival …

Genome-Wide Profiling Of Novel Conserved Zea Mays Micrornas Along With Their Key Biological, Molecular And Cellular Targets And Validation Using An Rt-Pcr Platform, Abdul Baqi, Sami Ullah, Muhammad Ayub, Muhammad Zafar Saleem, Ghulam Mustafa Khan, Asad Ullah

Karbala International Journal of Modern Science

MicroRNAs (miRNAs), which are typically non-coding RNAs that start off as endogenous molecules and regulate post-transcriptional levels of gene expression by mRNA degradation or translational repression. They are 18–26 nucleotides long, evolutionarily conserved and essential for predicting novel miRNAs in a variety of plants. Maize (Zea mays) is a significant food and forage crop in the globe today. In the present study, many maize miRNAs have been found to be associated with both plant development and responses to stress. In this study, 66 unique conserved maize miRNAs from 65 different miRNA families were predicted using several genomics-based methods …

The Role Of Cu (0-0.03) And Zn (0.02) Substitution On The Structural, Optical And Magnetic Properties Of Mgo Nanoparticles, S. Naseem Shah, Atif Dawar, Yasmeen Bibi, Abid Ali, M. Asif Siddiqui

Karbala International Journal of Modern Science

The co-precipitation method was employed to prepared Cu (0-0.03) and Zn (0.02) dual doped MgO nanoparticles. The secondary phases of CuO and Cu₂O were observed along with the cubical phase of MgO. The doping induced effect was noticed for the crystallite size variations (14.39-19.89 nm). The morphological transformation from spherical to rice-like shape were observed. The estimated values of optical bandgap (4.66-4.45 eV) were well correlated with the crystallite size and dopant concentrations. The ferromagnetic ordering was observed at room temperature and the enchantment in the coercivity (142.27 Oe) with Zn (0.02) doping was noticed. Such type of …

An Empirical Investigation Of Online Grocery Shopping Behaviors Based On Different Generations, Jung-Im Seo

Faculty Publications

The Coronavirus 19 (COVID-19) pandemic has significantly impacted on consumers’ grocery shopping habits and lifestyles. Online grocery shopping is one of the promising ways to have little contact as well as increase convenience. For this reason, the sales and revenues of online grocery shopping have been dramatically increasing during the pandemic. The purpose of this study to explore online grocery shopping behaviors of different generations and their shopping intentions toward online grocery shopping during and after the pandemic. Data were collected from Amazon Mechanical Turk (MTurk) and Southeast region in U.S.A with convenience sample. All Generations know that online grocery …

The Santa Clara, 2024-01-19, Santa Clara University

The Santa Clara

No abstract provided.

Augusta: From Rna-Seq To Gene Regulatory Networks And Boolean Models, Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlar

Department of Biochemistry: Faculty Publications

Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of …

Effectiveness Of Mycorrhizae And Vermicompost Seed Inoculation For Germination, Vegetative Growth, Cannabinoid Content, And Cured Flower Weight Of Cbd-Rich Hemp (Cannabis Sativa L.), Hannah Boyer, Nicole Wagner, Merritt Drewery

Journal of Agricultural Hemp Research

Effective germination and vigorous growth of hemp cultivars is paramount to cultivators’ ability to produce high-quality hemp products. Beneficial bacteria and fungi are known symbionts to plants and are used in regenerative agriculture to increase plant health and crop yield. This pilot study investigated the effect of microbial seed inoculation on germination rate, plant height, cured flower weight, and cannabinoid content of cannabidiol (CBD)-rich hemp (Cannabis sativa L). The experiment included a control and the following treatments: 1) seed inoculation of Great White ^â Premium Mycorrhizae (GW), 2) seed inoculation of vermicompost (V), and 3) seed inoculation of Great …

Epstein-Barr Virus-Based Prognostic Model In Nodular Sclerosis Classic Hodgkin Lymphoma, Chen Jiang, Li-Yun Huang, Ji-Hao Zhou, Zhi-Ming Li, Yu Wang, Jian-Chang Fu, Qin Yan, Yu-Yuan Huang, Min Zuo, Shimin Hu, Robert Peter Gale, Yang Liang, Jing-Ping Yun, Yu-Hua Huang

Faculty, Staff and Student Publications

The role of Epstein-Barr virus (EBV) in lymphoma cells of nodular sclerosis classic Hodgkin lymphoma (NScHL) is controversial. Our aim was to explore this and establish a clinically feasible model for risk stratification. We interrogated data from 542 consecutive subjects with NScHL receiving ABVD therapy and demonstrated EBV-infection in their lymphoma cells with EBV-encoded small RNAs (EBERs) in situ hybridization. Subjects were divided into training and validation datasets. As data from the training dataset suggested EBERs-positivity was the only independent prognostic factor for both progression-free survival (PFS) and overall survival (OS), we developed corresponding prognostic models based on it. Our …