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The amazing life of Azaleah Lane
Azaleah loved her class field trip to the National Zoo in Washington D.C, and is looking forward to earning extra credit by building a diorama of a tiger in his natural habitat for extra credit--but before she can even begin her task she has to solve the mystery of her younger sister's favorite missing stuffed animal because her parents and older sister are too busy and Tiana is ready to throw a tantrum.
Book
Assessing multiple score functions in Rosetta for drug discovery
Rosetta is a computational software suite containing algorithms for a wide variety of macromolecular structure prediction and design tasks including small molecule protocols commonly used in drug discovery or enzyme design. Here, we benchmark RosettaLigand score functions and protocols in comparison to results of other software recently published in the Comparative Assessment of Score Functions (CASF-2016). The CASF-2016 benchmark covers a wide variety of tests including scoring and ranking multiple compounds against a target, ligand docking of a small molecule to a target, and virtual screening to extract binders from a compound library. Direct comparison to the score functions provided by CASF-2016 results shows that the original RosettaLigand score function ranks among the top software for scoring, ranking, docking and screening tests. Most notably, the RosettaLigand score function ranked 2/34 among other report score functions in CASF-2016. We additionally perform a ligand docking test with full sampling to mimic typical use cases. Despite improved performance of newer score functions in canonical protein structure prediction and design, we demonstrate here that more recent Rosetta score functions have reduced performance across all small molecule benchmarks. The tests described here have also been uploaded to the Rosetta scientific benchmarking server and will be run weekly to track performance as the code is continually being developed.
Journal Article
Ann fights for freedom : an Underground Railroad survival story
In 1854 in Eastern Maryland twelve-year-old Ann is a slave, grateful that her family is still all together; but when their master, in need of money, decides to sell Ann and her younger brother, their parents decide to take the dangerous step of running away north to freedom--a journey filled with danger, especially since they are not sure how to find the first station on the Underground Railroad.
Book
NF-κB Affects Proliferation and Invasiveness of Breast Cancer Cells by Regulating CD44 Expression
NF-κB plays an important role in cancer initiation and progression. CD44, a cell surface glycoprotein, is involved in many cellular processes including cell adhesion, migration and proliferation. However, whether and how the two molecules interact in breast cancer is not clear. In recent years, the up-regulation of CD44 has served as a marker for tumor initiating cells in breast cancer and other cancer types. Despite the important role of CD44 in cellular processes and cancer, the mechanism underlying CD44 up-regulation in cancers remains poorly understood. Previously, we have identified a novel cis-element, CR1, located upstream of the CD44 promoter. We demonstrated that NF-κB and AP-1 are key trans-acting factors that interact with CR1. Here, we further analyzed the role of NF-κB in regulating CD44 expression in triple negative breast cancer cells, MDA-MB-231 and SUM159. Inhibition of NF-κB by Bay-11-7082 resulted in a reduction in CD44 expression. CD44 repression via NF-κB inhibition consequently decreased proliferation and invasiveness of breast cancer cells. These findings provide not only new insight into the molecular mechanism underlying CD44 regulation but also potential therapeutic targets that may help eliminate chemo- and radiation-resistant cancer cells.
Journal Article
PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking
Water molecules at the protein-small molecule interface often form hydrogen bonds with both the small molecule ligand and the protein, affecting the structural integrity and energetics of a binding event. The inclusion of these ‘bridging waters’ has been shown to improve the accuracy of predicted docked structures; however, due to increased computational costs, this step is typically omitted in ligand docking simulations. In this study, we introduce a resource-efficient, Rosetta-based protocol named “PlaceWaters” to predict the location of explicit interface bridging waters during a ligand docking simulation. In contrast to other explicit water methods, this protocol is independent of knowledge of number and location of crystallographic waters in homologous structures. We test this method on a diverse protein-small molecule benchmark set in comparison to other Rosetta-based protocols. Our results suggest that this coarse-grained, structure-based approach quickly and accurately predicts the location of bridging waters, improving our ability to computationally screen drug candidates.
Journal Article
Ms. Marvel
Ms. Marvel is back - and she's magnificent! But there's no such thing as business as usual in Jersey City. Aliens are wreaking havoc in Kamala's corner of the world, and they seem weirdly interested in Ms. Marvel...and her family! Kamala is about to face a devastating loss - but with an alien invasion ravaging her neighborhood, she's not going to have much time to grieve. Even if Kamala saves her hometown, will her life ever be the same? And what's all this business about a \"Chosen One\"? Eisner Award-winner Saladin Ahmed (BLACK BOLT, EXILES) and rising star Minkyu Jung take the reins of one of Marvel's most beloved new characters, with the shocking start of an all-new era!
Book
Pharmacological blockade of ASCT2-dependent glutamine transport leads to antitumor efficacy in preclinical models
A small molecule selectively targeting the cell-surface glutamine transporter ASCT2 disrupts glutamine signaling and metabolism. This compound displays low toxicity and strong antitumor activity in preclinical
in vitro
and
in vivo
models, thus holding promise as a treatment for glutamine-dependent tumors in a clinical setting.
The unique metabolic demands of cancer cells underscore potentially fruitful opportunities for drug discovery in the era of precision medicine. However, therapeutic targeting of cancer metabolism has led to surprisingly few new drugs to date. The neutral amino acid glutamine serves as a key intermediate in numerous metabolic processes leveraged by cancer cells, including biosynthesis, cell signaling, and oxidative protection. Herein we report the preclinical development of V-9302, a competitive small molecule antagonist of transmembrane glutamine flux that selectively and potently targets the amino acid transporter ASCT2. Pharmacological blockade of ASCT2 with V-9302 resulted in attenuated cancer cell growth and proliferation, increased cell death, and increased oxidative stress, which collectively contributed to antitumor responses
in vitro
and
in vivo
. This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in oncology, representing a new class of targeted therapy and laying a framework for paradigm-shifting therapies targeting cancer cell metabolism.
Journal Article
The feminism book
\"Combines authoritative text with graphics and quotes from leading contributors in an introduction to more than eighty-five of the most important ideas, movements, and events that have defined feminism and feminist thought throughout history. Using the Big Ideas series' trademark combination of authoritative, accessible text and bold graphics, this book traces feminism and the feminist movement from its origins, through the suffragette movement of the 19th century, to recent developments such as the Everyday Sexism Project and the #MeToo movement. Entries explore and explain each idea, placing them in their social and cultural context. Packed with inspirational quotations, profiles of key individuals and turning points, and flowcharts and infographics explaining the most significant concepts clearly and simply, The Feminism Book is perfect for anyone with an interest in female empowerment.\" -- (Source of summary not specified)
Book
Cell Specific CD44 Expression in Breast Cancer Requires the Interaction of AP-1 and NFκB with a Novel cis-Element
Breast cancers contain a heterogeneous population of cells with a small percentage that possess properties similar to those found in stem cells. One of the widely accepted markers of breast cancer stem cells (BCSCs) is the cell surface marker CD44. As a glycoprotein, CD44 is involved in many cellular processes including cell adhesion, migration and proliferation, making it pro-oncogenic by nature. CD44 expression is highly up-regulated in BCSCs, and has been implicated in tumorigenesis and metastasis. However, the genetic mechanism that leads to a high level of CD44 expression in breast cancer cells and BCSCs is not well understood. Here, we identify a novel cis-element of the CD44 directs gene expression in breast cancer cells in a cell type specific manner. We have further identified key trans-acting factor binding sites and nuclear factors AP-1 and NFκB that are involved in the regulation of cell-specific CD44 expression. These findings provide new insight into the complex regulatory mechanism of CD44 expression, which may help identify more effective therapeutic targets against the breast cancer stem cells and metastatic tumors.
Journal Article