Allosteric Regulation Alters Carrier Domain Translocation in Pyruvate Carboxylase

Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate. The reaction occurs in two separate catalytic domains, coupled by the long-range translocation of a biotinylated carrier domain (BCCP). Here, we use a series of hybrid PC enzymes to examine multiple BCCP translocation pathways in PC. These studies reveal that the BCCP domain of PC adopts a wide range of translocation pathways during catalysis. Furthermore, the allosteric activator, acetyl CoA, promotes one specific intermolecular carrier domain translocation pathway. These results provide a basis for the ordered thermodynamic state and the enhanced carboxyl group transfer efficiency in the presence of acetyl CoA, and reveal that the allosteric effector regulates enzyme activity by altering carrier domain movement. Given the similarities with enzymes involved in the modular synthesis of natural products, the allosteric regulation of carrier domain movements in PC is likely to be broadly applicable to multiple important enzyme systems

Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information [preprint]

Since late 2019, the novel coronavirus SARS-CoV-2 has introduced a wide array of health challenges globally. In addition to a complex acute presentation that can affect multiple organ systems, increasing evidence points to long-term sequelae being common and impactful. The worldwide scientific community is forging ahead to characterize a wide range of outcomes associated with SARS-CoV-2 infection; however the underlying assumptions in these studies have varied so widely that the resulting data are difficult to compare. Formal definitions are needed in order to design robust and consistent studies of Long COVID that consistently capture variation in long-term outcomes. Even the condition itself goes by three terms, most widely Long COVID , but also COVID-19 syndrome (PACS) or, post-acute sequelae of SARS-CoV-2 infection (PASC) . In the present study, we investigate the definitions used in the literature published to date and compare them against data available from electronic health records and patient-reported information collected via surveys. Long COVID holds the potential to produce a second public health crisis on the heels of the pandemic itself. Proactive efforts to identify the characteristics of this heterogeneous condition are imperative for a rigorous scientific effort to investigate and mitigate this threat

Denoising Diffusion Restoration Tackles Forward and Inverse Problems for the Laplace Operator

Diffusion models have emerged as a promising class of generative models that map noisy inputs to realistic images. More recently, they have been employed to generate solutions to partial differential equations (PDEs). However, they still struggle with inverse problems in the Laplacian operator, for instance, the Poisson equation, because the eigenvalues that are large in magnitude amplify the measurement noise. This paper presents a novel approach for the inverse and forward solution of PDEs through the use of denoising diffusion restoration models (DDRM). DDRMs were used in linear inverse problems to restore original clean signals by exploiting the singular value decomposition (SVD) of the linear operator. Equivalently, we present an approach to restore the solution and the parameters in the Poisson equation by exploiting the eigenvalues and the eigenfunctions of the Laplacian operator. Our results show that using denoising diffusion restoration significantly improves the estimation of the solution and parameters. Our research, as a result, pioneers the integration of diffusion models with the principles of underlying physics to solve PDEs.Comment: 29 page

An improved high-throughput screening assay for tunicamycin sensitivity in Arabidopsis seedlings

Tunicamycin sensitivity assays are a useful method for studies of endoplasmic reticulum stress and the unfolded protein response in eukaryotic cells. While tunicamycin sensitivity and tunicamycin recovery assays have been previously described, these existing methods are time-consuming, labor intensive and subjected to mechanical wounding. This study shows an improved method of testing tunicamycin sensitivity in Arabidopsis using liquid Murashige and Skoog medium versus the traditional solid agar plates. Liquid medium bypasses the physical manipulation of seedlings, thereby eliminating the risk of potential mechanical damage and additional unwanted stress to seedlings. Seedlings were subjected to comparative treatments with various concentrations of tunicamycin on both solid and liquid media and allowed to recover. Determination of fresh weight, chlorophyll contents analysis and qRT-PCR results confirm the efficacy of using liquid medium to perform quantitative tunicamycin stress assays

Ocular manifestations and pathology of adult T-cell leukemia/lymphoma associated with human T-lymphotropic virus type 1

The human T-cell lymphotropic virus type 1 (HTLV-1), endemic in defined geographical areas around the world, is recognized as the etiologic agent of adult T-cell leukemia/lymphoma (ATL), or HTLV-1. ATL is a rare adult onset T-cell malignancy that is characterized by the presence of ATL flower cells with T-cell markers, HTLV-1 antibodies in the serum, and monoclonal integration of HTLV-1 provirus in affected cells. Ocular manifestations associated with HTLV-1 virus infection have been reported and include HTLV-1 uveitis and keratoconjunctivitis sicca, but reports of ocular involvement in ATL are exceedingly rare. This article describes the ocular manifestations and pathology of ATL. We also report for the first time a case of a 34-year-old male with systemic ATL and prominent atypical lymphoid cell infiltration in the choroid. To our knowledge, this is the first report defining prominent choroidal involvement as a distinct ocular manifestation of ATL. ATL may masquerade as a variety of other conditions, and molecular techniques involving microdissection and PCR have proven to be critical diagnostic tools. International collaboration will be needed to better understand the presentation and diagnosis of this rare malignancy

Small-molecule inhibitors of proteins involved in base excision repair potentiate the anti-tumorigenic effect of existing chemotherapeutics and irradiation

There has been a recent upsurge in the development of small-molecule inhibitors specific to DNA repair proteins or proteins peripherally involved in base excision repair and the DNA damage response. These specific, nominally toxic inhibitors are able to potentiate the effect of existing cancer cell treatments in a wide array of cancers. One of the largest obstacles to overcome in the treatment of cancer is incomplete killing with initial cancer treatments, leading to resistant cancer. The progression of our understanding of cancer and normal cell responses to DNA damage has allowed us to develop biomarkers that we can use to help us predict responses of cancers, more specifically target cancer cells and overcome resistance. Initial successes using these small-molecule DNA repair inhibitors in target-validation experiments and in the early stages of clinical trials indicate an important role for these inhibitors, and allow for the possibility of a future in which cancers are potentially treated in a highly specific, individual manner

A categorification of Morelli's theorem

We prove a theorem relating torus-equivariant coherent sheaves on toric varieties to polyhedrally-constructible sheaves on a vector space. At the level of K-theory, the theorem recovers Morelli's description of the K-theory of a smooth projective toric variety. Specifically, let $X$ be a proper toric variety of dimension $n$ and let M_\bR = \mathrm{Lie}(T_\bR^\vee)\cong \bR^n be the Lie algebra of the compact dual (real) torus T_\bR^\vee\cong U(1)^n. Then there is a corresponding conical Lagrangian \Lambda \subset T^*M_\bR and an equivalence of triangulated dg categories \Perf_T(X) \cong \Sh_{cc}(M_\bR;\Lambda), where \Perf_T(X) is the triangulated dg category of perfect complexes of torus-equivariant coherent sheaves on $X$ and \Sh_{cc}(M_\bR;\Lambda) is the triangulated dg category of complex of sheaves on M_\bR with compactly supported, constructible cohomology whose singular support lies in $\Lambda$. This equivalence is monoidal---it intertwines the tensor product of coherent sheaves on $X$ with the convolution product of constructible sheaves on M_\bR.Comment: 20 pages. This is a strengthened version of the first half of arXiv:0811.1228v3, with new results; the second half becomes arXiv:0811.1228v

Open Gromov-Witten Invariants of Toric Calabi-Yau 3-Folds

We present a proof of the mirror conjecture of Aganagic-Vafa [arXiv:hep-th/0012041] and Aganagic-Klemm-Vafa [arXiv:hep-th/0105045] on disk enumeration in toric Calabi-Yau 3-folds for all smooth semi-projective toric Calabi-Yau 3-folds. We consider both inner and outer branes, at arbitrary framing. In particular, we recover previous results on the conjecture for (i) an inner brane at zero framing in the total space of the canonical line bundle of the projective plane (Graber-Zaslow [arXiv:hep-th/0109075]), (ii) an outer brane at arbitrary framing in the resolved conifold (Zhou [arXiv:1001.0447]), and (iii) an outer brane at zero framing in the total space of the canonical line bundle of the projective plane (Brini [arXiv:1102.0281, Section 5.3]).Comment: 39 pages, 11 figure