Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system

Efficient and modular genome editing technologies that manipulate the genome of bacterial pathogens will facilitate the study of pathogenesis mechanisms. However, such methods are yet to be established for Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight. We identified a single type I-C CRISPR-Cas system in the Xoo genome and leveraged this endogenous defence system for high-efficiency genome editing in Xoo. Specifically, we developed plasmid components carrying a mini-CRISPR array, donor DNA, and a phage-derived recombination system to enable the efficient and programmable genome editing of precise deletions, insertions, base substitutions, and gene replacements. Furthermore, the type I-C CRISPR-Cas system of Xoo cleaves target DNA unidirectionally, and this can be harnessed to generate large genomic deletions up to 212 kb efficiently. Therefore, the genome-editing strategy we have developed can serve as an excellent tool for functional genomics of Xoo, and should also be applicable to other CRISPR-harbouring bacterial plant pathogens.     

Efficacy and Safety of Parecoxib/Phloroglucinol Combination Therapy Versus Parecoxib Monotherapy for Acute Renal Colic: A Randomized,Double-Blind Clinical Trial

To investigate whether the addition of phloroglucinol to parecoxib could improve the efficacy in patients with acute renal colic. Patients of acute renal colic were randomly allocated to receive intravenous Parecoxib 40 mg plus placebo or Parecoxib 40 mg plus phloroglucinol 80 mg, respectively. Pain intensity was recorded using a visual analog scale (VAS) before drug administration and 5, 15, 30, 60, and 120 min after treatment start. The primary outcome was the mean pain intensity difference (PID) at each checkpoint and the effectiveness of drugs (≥50 % decrease in VAS score at the end checkpoint). The need for rescue analgesics and the incidence of adverse effects were considered as secondary outcome of the study. Among 236 patients enrolled in the study, 119 patients received intravenous parecoxib plus placebo and 114 patients received intravenous parecoxib plus phloroglucinol, the remaining 3 patients given up treatment. Baseline demographics were similar between two groups. There are significant differences in the PID at 15 and 30 min between two groups (P _15 min = 0.011, P _30 min = 0.013). Rescue analgesics were required by 17 patients (14.3 %) receiving parecoxib, 7 patients (6.1 %) receiving parecoxib plus phloroglucinol (P = 0.041). There were no differences in PID at other checkpoints between two groups, as well as in the incidence of adverse events and the drug effectiveness. Parecoxib in combination with phloroglucinol for acute renal colic has a faster action, also reduces the demand of rescue analgesics.     

Cancer risk in individuals with intellectual disability in Sweden: A population-based cohort study

BackgroundA knowledge gap exists about the risk of cancer in individuals with intellectual disability (ID). The primary aim of this study was to estimate the cancer risk among individuals with ID compared to individuals without ID.Methods and findingsWe conducted a population-based cohort study of all children live-born in Sweden between 1974 and 2013 and whose mothers were born in a Nordic country. All individuals were followed from birth until cancer diagnosis, emigration, death, or 31 December 2016 (up to age 43 years), whichever came first. Incident cancers were identified from the Swedish Cancer Register. We fitted Cox regression models to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) as measures of cancer risk in relation to ID after adjusting for several potential confounders. We analyzed ID by severity, as well as idiopathic ID and syndromic ID separately. We performed a sibling comparison to investigate familial confounding. The study cohort included a total of 3,531,305 individuals, including 27,956 (0.8%) individuals diagnosed with ID. Compared with the reference group (individuals without ID and without a full sibling with ID), individuals with ID were in general more likely to be male. The median follow-up time was 8.9 and 23.0 years for individuals with ID and individuals without ID, respectively. A total of 188 cancer cases were identified among individuals with ID (incidence rate [IR], 62 per 1,000 person-years), and 24,960 among individuals in the reference group (IR, 31 per 1,000 person-years). A statistically significantly increased risk was observed for any cancer (HR 1.57, 95% CI 1.35–1.82; P < 0.001), as well as for several cancer types, including cancers of the esophagus (HR 28.4, 95% CI 6.2–130.6; P < 0.001), stomach (HR 6.1, 95% CI 1.5–24.9; P = 0.013), small intestine (HR 12.0, 95% CI 2.9–50.1; P < 0.001), colon (HR 2.0, 95% CI 1.0–4.1; P = 0.045), pancreas (HR 6.0, 95% CI 1.5–24.8; P = 0.013), uterus (HR 11.7, 95% CI 1.5–90.7; P = 0.019), kidney (HR 4.4, 95% CI 2.0–9.8; P < 0.001), central nervous system (HR 2.7, 95% CI 2.0–3.7; P < 0.001), and other or unspecified sites (HR 4.8, 95% CI 1.8–12.9; P = 0.002), as well as acute lymphoid leukemia (HR 2.4, 95% CI 1.3–4.4; P = 0.003) and acute myeloid leukemia (HR 3.0, 95% CI 1.4–6.4; P = 0.004). Cancer risk was not modified by ID severity or sex but was higher for syndromic ID. The sibling comparison showed little support for familial confounding. The main study limitations were the limited statistical power for the analyses of specific cancer types, and the potential for underestimation of the studied associations (e.g., due to potential underdetection or delayed diagnosis of cancer among individuals with ID).ConclusionsIn this study, we found that individuals with ID showed an increased risk of any cancer, as well as of several specific cancer types. These findings suggest that extended surveillance and early intervention for cancer among individuals with ID are warranted.

In a nationwide cohort study in Sweden, Qianwei Liu and co-workers report on cancer risk in people with intellectual disability.     

Plasma High-Mannose and Complex/Hybrid N-Glycans Are Associated with Hypercholesterolemia in Humans and Rabbits

N-glycans play important roles in various pathophysiological processes and can be used as clinical diagnosis markers. However, plasma N-glycans change and their pathophysiological significance in the setting of hypercholesterolemia, a major risk factor for atherosclerosis, is unknown. Here, we collected plasma from both hypercholesterolemic patients and cholesterol-fed hypercholesterolemic rabbits, and determined the changes in the whole-plasma N-glycan profile by electrospray ionization mass spectrometry. We found that both the hypercholesterolemic patients and rabbits showed a dramatic change in their plasma glycan profile. Compared with healthy subjects, the hypercholesterolemic patients exhibited higher plasma levels of a cluster of high-mannose and complex/hybrid N-glycans (mainly including undecorated or sialylated glycans), whereas only a few fucosylated or fucosylated and sialylated N-glycans were increased. Additionally, cholesterol-fed hypercholesterolemic rabbits also displayed increased plasma levels of high-mannose in addition to high complex/hybrid N-glycan levels. The whole-plasma glycan profiles revealed that the plasma N-glycan levels were correlated with the plasma cholesterol levels, implying that N-glycans may be a target for treatment of hypercholesterolemia.     

CaCO3 and SrCO3 bioprecipitation by fungi isolated from calcareous soil

The urease‐positive fungi Pestalotiopsis sp. and Myrothecium gramineum, isolated from calcareous soil, were examined for their properties of CaCO₃ and SrCO₃ biomineralization. After incubation in media amended with urea and CaCl₂ and/or SrCl₂, calcite (CaCO₃), strontianite (SrCO₃), vaterite in different forms [CaCO₃, (Ca_xSr_1?x)CO₃] and olekminskite [Sr(Sr,Ca)(CO₃)₂] were precipitated, and fungal ‘footprints’ were observed on mineral surfaces. The amorphous precipitate mediated by Pestalotiopsis sp. grown with urea and equivalent concentrations of CaCl₂ and SrCl₂ was identified as hydrated Ca and Sr carbonates by Fourier transform infrared spectroscopy. Liquid media experiments showed M. gramineum possessed the highest Sr²⁺ removal ability, and ～ 49% of supplied Sr²⁺ was removed from solution when grown in media amended with urea and 50 mM SrCl₂. Furthermore, this organism could also precipitate 56% of the available Ca²⁺ and 28% of the Sr²⁺ in the form of CaCO₃, SrCO₃ and (Ca_xSr_1?x)CO₃ when incubated in urea‐amended media and equivalent CaCl₂ and SrCl₂ concentrations. This is the first report of biomineralization of olekminskite and coprecipitation of Sr into vaterite mediated by fungi. These findings suggest that urease‐positive fungi could play an important role in the environmental fate, bioremediation or biorecovery of Sr or other metals and radionuclides that form insoluble carbonates.     

High Expression of Testes-Specific Protease 50 Is Associated with Poor Prognosis in Colorectal Carcinoma

Background

Testes-specific protease 50 (TSP50) is normally expressed in testes and abnormally expressed in breast cancer, but whether TSP50 is expressed in colorectal carcinoma (CRC) and its clinical significance is unclear. We aimed to detect TSP50 expression in CRC, correlate it with clinicopathological factors, and assess its potential diagnostic and prognostic value.

Methodology/Principal Findings

TSP50 mRNAs and proteins were detected in 7 CRC cell lines and 8 CRC specimens via RT-PCR and Western blot analysis. Immunohistochemical analysis of TSP50, p53 and carcinoembryonic antigen (CEA) with tissue microarrays composed of 95 CRCs, 20 colorectal adenomas and 20 normal colorectal tissues were carried out and correlated with clinicopathological characteristics and disease-specific survival for CRC patients. There was no significant correlation between the expression levels of TSP50 and p53 (P = 0.751) or CEA (P = 0.663). Abundant expression of TSP50 protein was found in CRCs (68.4%) while it was poorly expressed in colorectal adenomas and normal tissues (P<0.0001). Thus, CRCs can be distinguished from them with high specificity (92.5%) and positive predictive value (PPV, 95.6%). The survival of CRC patients with high TSP50 expression was significantly shorter than that of the patients with low TSP50 expression (P = 0.010), specifically in patients who had early-stage tumors (stage I and II; P = 0.004). Multivariate Cox regression analysis indicated that high TSP50 expression was a statistically significant independent risk factor (hazard ratio  = 2.205, 95% CI = 1.214–4.004, P = 0.009).

Conclusion

Our data demonstrate that TSP50 is a potential effective indicator of poor survival for CRC patients, especially for those with early-stage tumors.     

Protein Expression of Urate Transporters in Renal Tissue of Patients with Uric Acid Nephrolithiasis

URAT1 and GLUT9 are two primary urate transporters involved in the renal urate handling. Renal urate underexcretion was reported in uric acid stone formers (UASF) in previous clinical studies. The aim of this study was to investigate the clinical features and possible impact of protein expression of URAT1 and GLUT9 in renal tissues of patients with uric acid (UA) nephrolithiasis. 23 UASF, 27 patients with calcium oxalate (CaOx) stones, and 22 normal controls were enrolled in this study. Clinical data revealed that older age of onset, high plasma UA concentration, low urinary PH, and relative renal urate underexcretion were associated with UASF. By immunohistochemical or western blotting analysis, a significant increase in the relative expression quantity of URAT1 in renal tissue of UASF was found compared to patients with CaOx nephrolithiasis and normal controls. In conclusion, our results suggested that upregulated URAT1 protein expression might contribute to the relative urate underexcretion from the kidney of UASF.     

Modulation,Bioinformatic Screening,and Assessment of Small Molecular Peptides Targeting the Vascular Endothelial Growth Factor Receptor

Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) are important factors in tumor growth and metastasis. Molecular probes or drugs designed to target VEGF/VEGFR interactions are crucial in tumor molecular imaging and targeted therapy. Bioinformatic methods enable molecular design based on the structure of bio-macromolecules and their interactions. This study was aimed to identify tumor-targeting small-molecule peptides with high affinity for VEGFR using bioinformatics screening. The VEGFR extracellular immunoglobulin-like modules Ig1–Ig3 were used as the target to systematically alter the primary peptide sequence of VEGF_125–136. Molecular docking and surface functional group interaction methods were combined in an in silico screen for polypeptides, which in theory, would have higher affinities for VEGFR. In vitro receptor competition binding assays were used to assess the affinity of the putative VEGFR-binding polypeptides. Rhodamine-conjugated peptides were used to label and visualize peptide-binding sites on A549 cells. Using bioinformatic screening, we identified 20 polypeptides with potentially higher affinity for VEGFR. The polypeptides were capable of inhibiting the binding of ¹²⁵I-VEGF to VEGFR in a dose-dependent manner. The IC₅₀ values of QKRKRKKSRKKH and RKRKRKKSRYIVLS (80 and 185 nmol/L, respectively) were significantly lower than that of VEGF_125–136 (464 nmol/L); thus, the affinity of these peptides for VEGFR was 6- and 2.5-fold higher, respectively, than that of VEGF_125–136. Rhodamine labeling of A549 cells revealed peptide binding mainly on the plasma membrane and in the cytoplasm. Bioinformatic approaches hold promise for the development of molecular imaging probes. Using this approach, we designed two peptides that showed higher affinity toward VEGFR. These polypeptides may be used as molecular probes or drugs targeting VEGFR, which can be utilized in molecular imaging and targeted therapy of certain tumors.