Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum.

Key message We mapped 11 sorghum traits, identified 33 candidate genes, and found a grain yield gene (GID1) that regulates seed development and a grass-specific tillering gene (DUF1618) transferred to Striga hermonthica.

Periosteal Ewing Sarcoma: Imaging Features and Clinical Outcomes in 7 Patients.

OBJECTIVE: The aim of this study was to describe imaging features, treatment, and prognosis of patients with periosteal Ewing sarcoma (PES). MATERIALS AND METHODS: Seven patients with PES treated between 2001 and 2020 were studied retrospectively for presenting symptoms, imaging features, treatment, and prognosis. RESULTS: Among the 7 patients (mean age, 27.3 years) with local pain and/or mass of less than 6 months duration, 4 were males and 3 females (1.3:1). These surface tumors involved 3 long bones and 4 pelvic bones. Radiographs showed cortical erosions with 2 and CT with 4 long bone tumors. All 7 surface tumors showed normal marrow on MRI, and 4 tumors demonstrated normal marrow activity on 18FFDG fluorodeoxyglucose PET-CT. The only exception was a PES involving iliac bone with thin cortex and marrow extension, which demonstrated hypermetabolic marrow activity. All patients were treated initially with chemotherapy and optional radiation treatment with complete tumor resolution of a tibial PES in 1 patient. The remaining 2 patients with long bone PES had tumor resection and limb-salvage surgery and the 4 patients with pelvic bone PES had hemipelvectomy after chemotherapy/radiation treatment. Five patients were disease-free with long-term survival. A patient with a long bone PES and solitary lung metastasis at onset had tumor resection and metastasectomy with complete recovery without tumor recurrence. The 2 patients with pubic bone PES had complete recovery without tumor recurrence; however, the remaining 2 patients with iliac bone PES developed distant metastases and died within 2 years of diagnosis. CONCLUSIONS: Periosteal Ewing sarcoma arises in periosteum of bone and spares medullary cavity. As compared with its intramedullary counterpart, the tumor has better prognosis with long-term survival. Rarely, the surface tumor arising at a bone with thin cortex, such as iliac bone or scapula, may have medullary involvement. We have described our experience in diagnosis and clinical management in 7 patients of this rare surface variant of the more common intramedullary Ewing sarcoma.

Ewing sarcoma of Hoffa fat pad in the knee: a case report and review of the literature on primary intraarticular sarcomas and Hoffa fat pad masses.

Primary intraarticular sarcomas are rare. We describe a unique case of intraarticular Ewing sarcoma arising in Hoffa fat pad of knee in a woman. The patient was treated successfully with chemotherapy and left knee arthroplasty; however, the tumor recurred after 3 years.We review the literature on primary intraarticular sarcomas and Hoffa fat pad masses in the knee.

Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane.

Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.

TLR9 signalling activation via direct ligation and its functional consequences in CD4 + T cells.

CpG Oligodeoxynucleotides (ODNs) are established TLR9 ligands; however, their functional responses in CD4+ T cells are believed to be independent of TLR9 and MyD88. We studied ligand-receptor interactions of ODN 2216 and TLR9 in human CD4+ T cells and assessed their consequences in terms of TLR9 signalling and cell phenotype. We demonstrated that the uptake of ODN 2216, a synthetic TLR9 agonist, is controlled by TLR9 signalling molecules and results in an increase in the expression of TLR9 signalling molecules, regulated via a feedback mechanism. Next, the uptake of ODN 2216 resulted in TLR9 signalling dependent but MyD88 independent increase in expression of TGF-ß. Finally, ODN 2216 treated CD4+ T cells showed an anti-inflammatory phenotype that was similar to Th3 type of regulatory T cells. These Th3-like cells were able to suppress the proliferation of untreated CD4+ T cells. Collectively, our results demonstrate a direct and interdependent relationship between ODN 2216 uptake and TLR9 signalling in CD4+ T cells. Our findings thus pave the way for future research to explore direct modulation of adaptive immune cells, using innate immune ligands, to subvert exaggerated inflammatory responses.

Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes.

G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. However, the development of these types of specific compounds remain as a great challenge. In here, we have developed a compound with ability to specifically signal a certain c-MYC G4 DNA structure through a fluorescence light-up mechanism. Despite the compound's two binding sites on the G4 DNA structure, only one of them result in the fluorescence light-up effect. This G-tetrad selectivity proved to originate from a difference in flexibility that affected the binding affinity and tilt the compound out of the planar conformation required for the fluorescence light-up mechanism. The intertwined relation between the presented factors is likely the reason for the lack of examples using rational design to develop compounds with turn-on emission that specifically target certain G4 DNA structures. However, this study shows that it is indeed possible to develop such compounds and present insights into the molecular details of specific G4 DNA recognition and signaling to advance future studies of G4 biology.

Spindle Cell Lipoma Revisited: Common and Unusual Magnetic Resonance Imaging Findings in 54 Patients With New Observations.

ABSTRACT: The aims of the study were to study demographic data of patients with spindle cell lipoma and describe a spectrum of magnetic resonance imaging features of the tumor.

Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization.

The signal transducer and activator of transcription 3 (STAT3) protein is a master regulator of most key hallmarks and enablers of cancer, including cell proliferation and the response to DNA damage. G-Quadruplex (G4) structures are four-stranded noncanonical DNA structures enriched at telomeres and oncogenes' promoters. In cancer cells, stabilization of G4 DNAs leads to replication stress and DNA damage accumulation and is therefore considered a promising target for oncotherapy. Here, we designed and synthesized novel quinazoline-based compounds that simultaneously and selectively affect these two well-recognized cancer targets, G4 DNA structures and the STAT3 protein. Using a combination of in vitro assays, NMR, and molecular dynamics simulations, we show that these small, uncharged compounds not only bind to the STAT3 protein but also stabilize G4 structures. In human cultured cells, the compounds inhibit phosphorylation-dependent activation of STAT3 without affecting the antiapoptotic factor STAT1 and cause increased formation of G4 structures, as revealed by the use of a G4 DNA-specific antibody. As a result, treated cells show slower DNA replication, DNA damage checkpoint activation, and an increased apoptotic rate. Importantly, cancer cells are more sensitive to these molecules compared to noncancerous cell lines. This is the first report of a promising class of compounds that not only targets the DNA damage cancer response machinery but also simultaneously inhibits the STAT3-induced cancer cell proliferation, demonstrating a novel approach in cancer therapy.

Genomic 3D compartments emerge from unfolding mitotic chromosomes.

The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process.

The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines Their Interactions with G-Quadruplex DNA.

G-quadruplex (G4) DNA structures are linked to fundamental biological processes and human diseases, which has triggered the development of compounds that affect these DNA structures. However, more knowledge is needed about how small molecules interact with G4 DNA structures. This study describes the development of a new class of bis-indoles (3,3-diindolyl-methyl derivatives) and detailed studies of how they interact with G4 DNA using orthogonal assays, biophysical techniques, and computational studies. This revealed compounds that strongly bind and stabilize G4 DNA structures, and detailed binding interactions which for example, show that charge variance can play a key role in G4 DNA binding. Furthermore, the structure-activity relationships generated opened the possibilities to replace or introduce new substituents on the core structure, which is of key importance to optimize compound properties or introduce probes to further expand the possibilities of these compounds as tailored research tools to study G4 biology.

Clinical and epidemiological profile of patients infected by COVID-19 at a tertiary care centre in North India.

A worldwide outbreak of a respiratory illness, first detected in December 2019 in Wuhan city, Hubei province, China is ongoing. The disease is caused by a novel coronavirus, SARS-CoV-2 and on February 11, 2020, was officially named Coronavirus Disease 2019 (COVID-19) by the World Health Organization. Within few weeks, it has spread globally to the extent that World Health Organization declared it as a global pandemic on March 11, 2020. India's first positive case was reported on January 30th in Kerala. Before March 3rd, India had 3 cases of coronavirus in Kerala all of which were treated and discharged. On March 3rd, India's 4th case was diagnosed in the state of Rajasthan. Indian government had announced a number of preventive measures to minimize the entry and spread of coronavirus. On March 3rd, India announced the suspension of all visas issued to Italy, Iran, South Korea and Japan. India banned international flights from March 22nd. A 21-day lockdown across the country was imposed from March 26th, which later got further extended. Rigorous contact tracing and tracking of COVID patients and monitoring home quarantine helped in preventing community transmission. The aim of this work is to describe the experience with clinical and epidemiologic features, as well as with the management of COVID-19 patients in north India. This is a descriptive study of the 17 COVID-19 infected patients confirmed with polymerase chain reaction (PCR) and admitted to a tertiary care centre in India from March 11th 2020 to April 16th 2020. The present work also provides insight in to treatment provided and final outcome of the patients infected with COVID-19 in India. Laboratory investigations in COVID-19 patients in the Indian subcontinent reveal lymphopenia as predominant finding in hemogram. Patients with older age and associated comorbidities (COPD, hypertension and diabetes) seem to have greater risk for lung injury, thereby requiring oxygen support during the course of disease.

Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea.

Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association and in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding (CAB) protein-coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.

Direct Engagement of TLR9 Ligand with T Helper Cells Leads to Cell Proliferation & Up-regulation of Cytokines.

PURPOSE: Toll like receptor (TLR) engagement is primarily a function of the innate immune cells. The purpose of the study was to assess direct uptake of ODN 2216 in T helper cells and effects on cell proliferation and cytokine expression. METHODS: We isolated CD4+ CD25- T helper cells by magnetic sorting and studied the uptake of ODN 2216 using flow cytometry and confocal microscopy. We then studied the effect of ODN 2216 engagement on cell proliferation and cytokine expression using flow cytometry and gene expression of TLR9 signaling genes using real time RT-PCR. RESULTS: We made a chance observation that purified T helper cells from healthy individuals consistently bind to the TLR9 ligand ODN 2216. In PBMCs, on the other hand, 98% of monocytes preferentially bound to ODN 2216 FITC, indicating that they competed with the lymphocytes. We confirmed intracellular localization of ODN 2216 FITC as well as intracellular expression of TLR9 in Thelper cells. Furthermore, ODN 2216 FITC was also co-localized with the lysosomal membrane associated protein 1. The uptake of TLR9 ligand culminated in cellular proliferation, up-regulation of cytokines and increased mRNA expression of TLR9 and IRF7 in T helper cells, in the absence of antigen presenting cells. ODN 2216 uptake was inhibited by promethazine as well as by TLR9 antagonist. CONCLUSIONS: Our results show a direct engagement of TLR9 ligand in T helper cells and suggest involvement of TLR9 signalling in CD4+T cells, which may envisage novel targets for TLR inhibitors.

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps.

Hi-C experiments generate data in form of large genome contact maps (Hi-C maps). These show that chromosomes are arranged in a hierarchy of three-dimensional compartments. But to understand how these compartments form and by how much they affect genetic processes such as gene regulation, biologists and bioinformaticians need efficient tools to visualize and analyze Hi-C data. However, this is technically challenging because these maps are big. In this paper, we remedied this problem, partly by implementing an efficient file format and developed the genome contact map explorer platform. Apart from tools to process Hi-C data, such as normalization methods and a programmable interface, we made a graphical interface that let users browse, scroll and zoom Hi-C maps to visually search for patterns in the Hi-C data. In the software, it is also possible to browse several maps simultaneously and plot related genomic data. The software is openly accessible to the scientific community.

Flexible Versus Rigid G-Quadruplex DNA Ligands: Synthesis of Two Series of Bis-indole Derivatives and Comparison of Their Interactions with G-Quadruplex DNA.

Small molecules that target G-quadruplex (G4) DNA structures are not only valuable to study G4 biology but also for their potential as therapeutics. This work centers around how different design features of small molecules can affect the interactions with G4 DNA structures, exemplified by the development of synthetic methods to bis-indole scaffolds. Our synthesized series of bis-indole scaffolds are structurally very similar but differ greatly in the flexibility of their core structures. The flexibility of the molecules proved to be an advantage compared to locking the compounds in the presumed bioactive G4 conformation. The flexible derivatives demonstrated similar or even improved G4 binding and stabilization in several orthogonal assays even though their entropic penalty of binding is higher. In addition, molecular dynamics simulations with the c-MYC G4 structure showed that the flexible compounds adapt better to the surrounding. This was reflected by an increased number of both stacking and polar interactions with both the residues in the G4 DNA structure and the DNA residues just upstream of the G4 structure.

Primary Osteosarcoma in the Elderly Revisited: Current Concepts in Diagnosis and Treatment.

PURPOSE OF REVIEW: Osteosarcoma is mostly seen in bones of children and young adults. When it occurs in older persons, the tumor is considered secondary usually complicating Paget disease or irradiated bone. However, there is a second incidence peak of primary osteosarcoma later in life when these tumors occur de novo. This article describes the clinical, imaging, and treatment of POS in older patients, including demographic data of patients from our institution. FINDINGS: We present our experience with 920 cases of osteosarcoma that were seen between 1984 and 2003 at the University of Texas MD Anderson Cancer Center in Houston, TX, USA. Among the 868 primary osteosarcoma of bones, there were 100 (11.52%), which comprised 69% of the tumors in patients over the age of 50 years. Older patients with primary osteosarcoma tend to have relatively more common axial skeleton involvement, have more distant disease, and are difficult to treat because of concomitant comorbidities. Despite that, most adult patients treated with chemotherapy have shown good results with longer disease-free survival. A lytic bone lesion seen in radiographs of elderly patients should include primary osteosarcoma among differential diagnoses. Radical surgery and chemotherapy seem to ensure long-term disease-free survival in most cases. The elderly patients with POS in pelvis, spine, and upper extremities and those with distant disease (metastases) have worse prognosis.

Structural-Mechanical and Biochemical Functions of Classical Cadherins at Cellular Junctions: A Review and Some Hypotheses.

This article begins with a general review of cell adhesion molecules (CAMs) and narrows the focus down progressively to the cadherins (calcium binding-dependent CAMs), classifications of subfamilies of the cadherins, type I (E- and N-) cadherins, evolutionary relationships amongst cadherins, structural-mechanical and functional consequences of calcium binding to the cadherins, differential molecular interactions involving the extracellular (ecto) and intracellular (cytoplasmic) domains of the cadherins, multiple adherence-related homophilic and heterophilic interactions and associated functions of E- and N-cadherin in organismal development and disease and cadherin trafficking and membrane rafts. It ends by summarizing multiple perspectives and hypotheses concerning different aspects of cadherin structure, stability and function.

Fullerenol-Based Intracellular Delivery of Methotrexate: A Water-Soluble Nanoconjugate for Enhanced Cytotoxicity and Improved Pharmacokinetics.

Derivatization of fullerenes to polyhydroxylated fullerenes, i.e., fullerenols (FLU), dramatically decreases their toxicity and has been reported to enhance the solubility as well as cellular permeability. In this paper, we report synthesis of FLU as nanocarrier and subsequent chemical conjugation of Methotrexate (MTX) to FLU with a serum-stable and intracellularly hydrolysable ester bond between FLU and MTX. The conjugate was characterized for physiochemical attributes, micromeritics, drug-loading, and drug-release and evaluated for cancer cell-toxicity, cellular-uptake, hemocompatibility, protein binding, and pharmacokinetics. The developed hemocompatible FL-MTX offered lower protein binding vis-à-vis naïve drug and substantially higher drug loading. The conjugate offered pH-dependent release of 38.20 ± 1.19% at systemic pH and 85.67 ± 3.39% at the cancer cell pH. FLU-MTX-treated cells showed significant reduction in IC50 value vis-à-vis the cells treated with pure MTX. Analogously, the results from confocal scanning laser microscopy also confirmed the easy access of the dye-tagged FLU-MTX conjugate to the cell interiors. In pharmacokinetics, the AUC of MTX was enhanced by approx. 6.15 times and plasma half-life was enhanced by 2.45 times, after parenteral administration of single equivalent dose in rodents. FLU-MTX offered enhanced availability of drug to the biological system, meanwhile improved the cancer-cell cytotoxicity, sustained the effective plasma drug concentrations, and offered substantial compatibility to erythrocytes.

Role of matrix metalloproteinase 13 gene expression in the evaluation of radiation response in oral squamous cell carcinoma.

BACKGROUND: Matrix Metalloproteinase 13 (MMP13) is a member of collagenase family and it is involved in the degradation of extracellular matrix and basement membrane protein. It is thought to be associated with tumor invasion and metastasis. Elevated MMP13 expression has been found in carcinoma of the breast, urinary bladder, head and neck and others. It is observed that MMP13 gene is also correlated with radiation response in OSCC (Oral squamous cell carcinoma) cell line based study. The present study correlates the MMP13 expressions with clinicopathological parameters and radiation response in OSCC patients. MATERIALS AND METHODS: The MMP13 mRNA levels were determined by employing qRT-PCR (real-time quantitative reverse transcriptase-polymerase chain reaction). RESULTS: We observed high expression of MMP13 mRNA in OSCC patients when compared with matched controls. Statistically significant up regulation of MMP13 mRNA expression was found in tobacco chewers, advanced T-stage (p < 0.001) and lymph node metastasis (p < 0.01). MMP13 mRNA levels were also elevated in non responders as compared to responders to radiation treatment. CONCLUSIONS: To the best of our knowledge, this is the first report that indicates role of MMP13 in radiation response in OSCC patients and could be used as potential bio-marker for radiotherapy treatment in OSCC patients.

Myxoinflammatory Fibroblastic Sarcoma: Clinical, Imaging, Management and Outcome in 29 Patients.

OBJECTIVE: This retrospective study was undertaken to highlight clinical and magnetic resonance imaging features of myxoinflammatory fibroblastic sarcoma. METHODS: The clinical records of 29 patients (14 men and 15 women) were analyzed. RESULTS: The soft tissue tumors involved hand, wrist, foot and ankle in 21 patients, more proximal extremities in 7 patients, and neck in 1 patient. The tumors were subcutaneous in 11 patients, and intramuscular in 15 patients. On magnetic resonance imaging, these tumors had nonspecific features suggestive of benign and malignant lesions. An unusual tumor in hand indicated infection, whereas an intraarticular knee tumor mimicked pigmented villonodular synovitis. All tumors were surgically resected. CONCLUSIONS: Myxoinflammatory fibroblastic sarcoma, a rare low-grade subcutaneous soft tissue tumor of distal extremities with high local recurrence after resection can mimic several benign and malignant lesions on histopathology and imaging. Rarely, it can arise in muscles and tendons, occur in nonacral sites, be aggressive, and even metastasize. In most cases, surgical resection with wide margins can be curative with low local recurrence.