Effects of maize and soybean intercropping on soil phosphorus bioavailability and microbial community structure in rhizosphere.

To investigate the effect of maize/soybean intercropping on rhizosphere soil microbial communities and phosphorus (P) bioavailability, we examined the changes of soil bioavailable P fractions and microbial community characteristics in the monoculture and intercropping systems based on high-throughput sequencing. The results showed that maize/soybean intercropping increased the contents of rhizosphere soil organic matter (SOM), available phosphorus (AP), microbial biomass phosphorus (MBP), and aboveground biomass. The increase of AP was mainly related to the increasing enzyme extracted phosphorus (Enzyme-P) and hydrochloric acid extracted phosphorus (HCl-P) contents. The dominant bacterial phyla under each treatment were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, while the dominant bacterial genera were Nocardioides, Solirubacter, Sphingomonas and Arthrobacter, with Proteobacteria and Sphingomonas having the highest relative abundance. The relative abundance of Proteobacteria and Sphingomonas in intercropping maize rhizosphere soil was significantly higher than that in monoculture, and that of Proteobacteria in intercropping soybean rhizosphere soil was significantly higher than monoculture. Soil properties and P fractions were closely related to the rhizosphere soil microbial composition. In all, maize/soybean intercropping could affect the rhizosphere soil P bioavailability by altering the structure of rhizosphere microbial communities.

CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue.

Pooled genetic screens are powerful tools to study gene function in a high-throughput manner. Typically, sequencing-based screens require cell lysis, which limits the examination of critical phenotypes such as cell morphology, protein subcellular localization, and cell-cell/tissue interactions. In contrast, emerging optical pooled screening methods enable the investigation of these spatial phenotypes in response to targeted CRISPR perturbations. In this study, we report a multi-omic optical pooled CRISPR screening method, which we have named CRISPRmap. Our method combines a novel in situ CRISPR guide identifying barcode readout approach with concurrent multiplexed immunofluorescence and in situ RNA detection. CRISPRmap barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency, while reducing both dependency on third party proprietary sequencing reagents and assay cost. Notably, we conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes involved in the homologous recombination and Fanconi anemia pathways investigating how nucleotide variants in those genes influence DNA damage signaling and cell cycle regulation following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy. Approximately a million cells were profiled with our multi-omic approach, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance. Furthermore, our approach effectively distinguished barcodes of a pooled library in tumor tissue, and we coupled it with cell-type and molecular phenotyping by cyclic immunofluorescence. Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.

Proper Partial Pressure of Arterial Oxygen for Patients with Traumatic Brain Injury.

BACKGROUND The partial pressure of arterial oxygen (PaO2) is critical to the outcome of patients with traumatic brain injury (TBI). However, it is not clear what range of PaO2 should be maintained to improve patient outcome. The aim of this study was to explore the PaO2 value needed in the acute phase of TBI and provide new evidence for clinical practice. MATERIAL AND METHODS A total of 153 patients with TBI were enrolled retrospectively. Univariate and multivariate logistic regression analyses were conducted on sex, Glasgow Coma Scale (GCS) score on admission, PaO2 within 6 h of admission, oxygenation index, and other factors. The Glasgow Outcome Score (GOS) of the patient at discharge was used as an indicator of outcome. The good outcome group had GOS ≥4, and the poor outcome group had GOS <4. RESULTS The 153 patients were divided into a good outcome group (n=62) and poor outcome group (n=91). There was a significant difference in sex, admission GCS, surgery, airway status, PaO2, and oxygen index within 6 h of admission between the 2 groups. Logistic regression analysis showed that PaO2 <60 mmHg, male sex, and admission GCS score of 3 to 12 were independent risk factors for a poor outcome. CONCLUSIONS Patients with TBI having PaO2 <60 mmHg within 6 h after admission were more likely to have poor outcomes. The upper limit value of PaO2 that affects the outcome of TBI in patients has not been found.

Intracranial Pressure during External Ventricular Drainage Weaning Is an Outcome Predictor of Traumatic Brain Injury.

External ventricular drainage (EVD) is widely used in patients with a traumatic brain injury (TBI). However, the EVD weaning trial protocol varies and insufficient studies focus on the intracranial pressure (ICP) during the weaning trial. We aimed to establish the relationship between ICP during an EVD weaning trial and the outcomes of TBI. We enrolled 37 patients with a TBI with an EVD from July 2018 to September 2019. Among them, 26 were allocated to the favorable outcome group and 11 to the unfavorable outcome group (death, post-traumatic hydrocephalus, persistent vegetative state, and severe disability). Groups were well matched for sex, pupil reactivity, admission Glasgow Coma Scale score, Marshall computed tomography score, modified Fisher score, intraventricular hemorrhage, EVD days, cerebrospinal fluid output before the weaning trial, and the complications. Before and during the weaning trial, we recorded the ICP at 1-hour intervals to calculate the mean ICP, delta ICP, and ICP burden, which was defined as the area under the ICP curve. There were significant between-group differences in the age, surgery types, and intensive care unit days (p = 0.045, p = 0.028, and p = 0.004, respectively). During the weaning trial, 28 (75.7%) patients had an increased ICP. Although there was no significant difference in the mean ICP before and during the weaning trial, the delta ICP was higher in the unfavorable outcome group (p = 0.001). Moreover, patients who experienced death and hydrocephalus had a higher ICP burden, which was above 20 mmHg (p = 0.016). Receiver operating characteristic analyses demonstrated the predictive ability of these variables (area under the curve [AUC] = 0.818 [p = 0.002] for delta ICP and AUC = 0.758 [p = 0.038] for ICP burden > 20 mmHg). ICP elevation is common during EVD weaning trials in patients with TBI. ICP-related parameters, including delta ICP and ICP burden, are significant outcome predictors. There is a need for larger prospective studies to further explore the relationship between ICP during EVD weaning trials and TBI outcomes.

Differential radiation response between normal astrocytes and glioma cells revealed by comparative transcriptome analysis.

Normal astrocytes are more resistant to radiation than glioma cells. Radiation-resistant glioma cells and normal astrocytes usuallly share similar mechanisms of radioresistance. Investigation of the underlying mechanisms of differential radiation response between normal astrocytes and glioma cells is thus significant for improvement of glioma treatment. Here, we report on the differential radiation responses between normal astrocytes and glioma cells at the transcriptome level. Human astrocytes (HA) and U251 glioma cell lines were used as in vitro models. The transcriptome profiles of radiation-treated and nontreated HA and U251 cells were generated by next-generation sequencing. In total, 296 mRNAs and 224 lncRNAs in HA and 201 mRNAs and 107 lncRNAs in U251 were found to be differentially expressed after radiation treatment. Bioinformatics analyses indicated that radiation causes similar alterations in HA and U251 cells, while several key pathways involved in cancer development and radiation resistance, including P53, TGF-ß, VEGF, Hippo and serotonergic synapse pathways, were oppositely regulated by radiation treatment, suggesting their important role in this process. Furthermore, we showed the critical role of Hippo/YAP signaling in radiation resistance of glioma cells. In summary, our findings revealed novel insights about differential responses between normal astrocytes and glioma cells. Our work suggested that YAP inhibitor could not be used in combination with radiation for glioma treatment.