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  • Artificial Soils Reveal Individual Factor Controls on Microbial Processes 

    Del Valle, Ilenne; Gao, Xiaodong; Ghezzehei, Teamrat A.; Silberg, Jonathan J.; Masiello, Caroline A. (2022)
    Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil ...
  • Real-time detection of response regulator phosphorylation dynamics in live bacteria 

    Butcher, Ryan J.; Tabor, Jeffrey J. (2022)
    Bacteria utilize two-component system (TCS) signal transduction pathways to sense and adapt to changing environments. In a typical TCS, a stimulus induces a sensor histidine kinase (SHK) to phosphorylate a response regulator (RR), which then dimerizes and activates a transcriptional response. Here, we demonstrate that oligomerization-dependent ...
  • Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions 

    Wang, Kaiyuan; Escobar, Mario; Li, Jing; Mahata, Barun; Goell, Jacob; (2022)
    Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer–promoter pairs. Here, ...
  • Modes of Selection in Tumors as Reflected by Two Mathematical Models and Site Frequency Spectra 

    Kurpas, Monika K.; Kimmel, Marek (2022)
    The tug-of-war model was developed in a series of papers of McFarland and co-authors to account for existence of mutually counteracting rare advantageous driver mutations and more frequent slightly deleterious passenger mutations in cancer. In its original version, it was a state-dependent branching process. Because of its formulation, the tug-of-war ...
  • Evaluation of a Point-of-Care Test for Bilirubin in Malawi 

    Shapiro, Alyssa; Anderson, Jessica; Mtenthaonga, Prince; Kumwenda, Watson; Bond, Meaghan; (2022)
    OBJECTIVES: BiliSpec is a low-cost spectrophotometric reader and disposable paper-based strip to quantify total serum bilirubin from several blood drops. This study was a prospective evaluation of BiliSpec in 2 neonatal wards in Malawi compared with a reference standard bilirubinometer over a large range of bilirubin and hematocrit levels. METHODS: ...
  • Assessing Gq-GPCR–induced human astrocyte reactivity using bioengineered neural organoids 

    Cvetkovic, Caroline; Patel, Rajan; Shetty, Arya; Hogan, Matthew K.; Anderson, Morgan; (2022)
    Astrocyte reactivity can directly modulate nervous system function and immune responses during disease and injury. However, the consequence of human astrocyte reactivity in response to specific contexts and within neural networks is obscure. Here, we devised a straightforward bioengineered neural organoid culture approach entailing transcription ...
  • Multiplexed high-throughput localized electroporation workflow with deep learning–based analysis for cell engineering 

    Patino, Cesar A.; Pathak, Nibir; Mukherjee, Prithvijit; Park, So Hyun; Bao, Gang; (2022)
    Manipulation of cells for applications such as biomanufacturing and cell-based therapeutics involves introducing biomolecular cargoes into cells. However, successful delivery is a function of multiple experimental factors requiring several rounds of optimization. Here, we present a high-throughput multiwell-format localized electroporation device ...
  • Evaluating the physicochemical effects of conjugating peptides into thermogelling hydrogels for regenerative biomaterials applications 

    Pearce, Hannah A; Jiang, Emily Y; Swain, Joseph W R; Navara, Adam M; Guo, Jason L; (2021)
    Thermogelling hydrogels, such as poly(N-isopropylacrylamide) [P(NiPAAm)], provide tunable constructs leveraged in many regenerative biomaterial applications. Recently, our lab developed the crosslinker poly(glycolic acid)-poly(ethylene glycol)-poly(glycolic acid)-di(but-2-yne-1,4-dithiol), which crosslinks P(NiPAAm-co-glycidyl methacrylate) via ...
  • Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces 

    Ameruoso, Andrea; Villegas Kcam, Maria Claudia; Cohen, Katherine Piper; Chappell, James (2022)
    The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic ...
  • Exploring the Photophysical Properties of UiO-67 MOF Doped with Rhenium Carbonyl Complexes 

    Ling, Kexin; Ogle, Meredith M.; Flores, Erick; Godoy, Fernando; Martí, Angel A. (2022)
    Directly coordinating transition metal catalysts to the linkers of stable metal organic frameworks (MOFs) is a sleek solution to increasing the longevity of the catalyst. Photoluminescence metal complexes incorporated in MOFs have risen in interest lately. Particularly, Re(bpydc)(CO)3Cl (bpydc = 2,2’-bipyridine-5,5’-dicarboxylic acid) doped zirconium-based ...
  • Tissue Engineering and Regulatory Science 

    Zhao, Peng; Liu, Wenbo; Tian, Jiaxin; Shi, Xinli; Gu, Xiaosong; (2022)
  • A 3D printable perfused hydrogel vascular model to assay ultrasound-induced permeability 

    Royse, Madison K.; Means, A. Kristen; Calderon, Gisele A.; Kinstlinger, Ian S.; He, Yufang; (2022)
    The development of an in vitro model to study vascular permeability is vital for clinical applications such as the targeted delivery of therapeutics. This work demonstrates the use of a perfusion-based 3D printable hydrogel vascular model as an assessment for endothelial permeability and its barrier function. Aside from providing a platform that more ...
  • Additive manufacturing for the development of optical/photonic systems and components 

    Berglund, Gregory; Wisniowiecki, Anna; Gawedzinski, John; Applegate, Brian; Tkaczyk, Tomasz S. (2022)
    The ambition of this review is to provide an up-to-date synopsis of the state of 3D printing technology for optical and photonic components, to gauge technological advances, and to discuss future opportunities. While a range of approaches have been developed and some have been commercialized, no single approach can yet simultaneously achieve small ...
  • A wireless millimetric magnetoelectric implant for the endovascular stimulation of peripheral nerves 

    Chen, Joshua C.; Kan, Peter; Yu, Zhanghao; Alrashdan, Fatima; Garcia, Roberto; (2022)
    Implantable bioelectronic devices for the simulation of peripheral nerves could be used to treat disorders that are resistant to traditional pharmacological therapies. However, for many nerve targets, this requires invasive surgeries and the implantation of bulky devices (about a few centimetres in at least one dimension). Here we report the design ...
  • National scale of neonatal CPAP to district hospitals in Malawi improves survival for neonates weighing between 1.0 and 1.3 kg 

    Carns, Jennifer; Liaghati-Mobarhan, Sara; Asibon, Aba; Chalira, Alfred; Lufesi, Norman; (2022)
    Objective To determine whether a national quality improvement programme implementing continuous positive airway pressure (CPAP) at government hospitals in Malawi improved outcomes for neonates prioritised by an algorithm recommending early CPAP for infants weighing 1.0–1.3 kg (the 50th percentile weight at 30 weeks’ gestation). Design The analysis ...
  • Significance of aortoseptal angle anomalies to left ventricular hemodynamics and subaortic stenosis: A numerical study 

    Shar, Jason A.; Keswani, Sundeep G.; Grande-Allen, K. Jane; Sucosky, Philippe (2022)
    Purpose Discrete subaortic stenosis (DSS) is an obstructive cardiac disease caused by a membranous lesion in the left ventricular (LV) outflow tract (LVOT). Although its etiology is unknown, the higher prevalence of DSS in LVOT anatomies featuring a steep aortoseptal angle (AoSA) suggests a potential role for hemodynamics. Therefore, the objective ...
  • Evidence-based biomaterials research 

    Zhang, Kai; Ma, Bin; Hu, Kaiyan; Yuan, Bo; Sun, Xin; (2022)
    The fast development of biomaterials science and engineering has generated significant number of studies and publications as well as tremendous amount of research data. A methodology is needed to translate such research data and results to validated scientific evidence. This article for the first time proposes the concept and methodology of evidence-based ...
  • Current progress and open challenges for applying deep learning across the biosciences 

    Sapoval, Nicolae; Aghazadeh, Amirali; Nute, Michael G.; Antunes, Dinler A.; Balaji, Advait; (2022)
    Deep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future perspectives of DL on five broad areas: protein structure prediction, protein function prediction, genome ...
  • Correlation of nuclear pIGF-1R/IGF-1R and YAP/TAZ in a tissue microarray with outcomes in osteosarcoma patients 

    Molina, Eric R.; Chim, Letitia K.; Lamhamedi-Cherradi, Salah-Eddine; Mohiuddin, Sana; McCall, David; (2022)
    Osteosarcoma (OS) is a genetically diverse bone cancer that lacks a consistent targetable mutation. Recent studies suggest the IGF/PI3K/mTOR pathway and YAP/TAZ paralogs regulate cell fate and proliferation in response to biomechanical cues within the tumor microenvironment. How this occurs and their implication upon osteosarcoma survival, remains ...
  • Bone-Specific Enhancement of Antibody Therapy for Breast Cancer Metastasis to Bone 

    Tian, Zeru; Yu, Chenfei; Zhang, Weijie; Wu, Kuan-Lin; Wang, Chenhang; (2022)
    Despite the rapid evolution of therapeutic antibodies, their clinical efficacy in the treatment of bone tumors is hampered due to the inadequate pharmacokinetics and poor bone tissue accessibility of these large macromolecules. Here, we show that engineering therapeutic antibodies with bone-homing peptide sequences dramatically enhances their ...

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