Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering.

Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental challenge. To resolve this challenge, here we present Protein Mutational Effect Predictor (ProMEP), a general and multiple sequence alignment-free method that enables zero-shot prediction of mutation effects. A multimodal deep representation learning model embedded in ProMEP was developed to comprehensively learn both sequence and structure contexts from ~160 million proteins. ProMEP achieves state-of-the-art performance in mutational effect prediction and accomplishes a tremendous improvement in speed, enabling efficient and intelligent protein engineering. Specifically, ProMEP accurately forecasts mutational consequences on the gene-editing enzymes TnpB and TadA, and successfully guides the development of high-performance gene-editing tools with their engineered variants. The gene-editing efficiency of a 5-site mutant of TnpB reaches up to 74.04% (vs 24.66% for the wild type); and the base editing tool developed on the basis of a TadA 15-site mutant (in addition to the A106V/D108N double mutation that renders deoxyadenosine deaminase activity to TadA) exhibits an A-to-G conversion frequency of up to 77.27% (vs 69.80% for ABE8e, a previous TadA-based adenine base editor) with significantly reduced bystander and off-target effects compared to ABE8e. ProMEP not only showcases superior performance in predicting mutational effects on proteins but also demonstrates a great capability to guide protein engineering. Therefore, ProMEP enables efficient exploration of the gigantic protein space and facilitates practical design of proteins, thereby advancing studies in biomedicine and synthetic biology.

Giant desmoplastic small round cell tumor of the abdomen: A case report.

Background: Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, mesenchymal malignancy of a separate clinicopathological entity. It has a predilection for young men, with no evidence of any ethnic predilection. The current diagnostic gold standard for DSRCT includes histopathologic, immunohistochemical, and cytogenetic studies in order to confirm the variable phenotypic expression and characteristic chromosomal translocation. Case summary: A 65-year-old man presented with a sensation of an abdominal mass and a presentation of an incomplete bowel obstruction. Initial lab tests were in the normal range except for carbohydrate antigen. Contrast-enhanced CT showed that a large, mass-confounding density was occupied in the omentum majus area of the middle and lower abdominal wall. A 3D reconstruction of the images was performed to clarify the relationship between the tumor and the colon and was confirmed by a colonoscopy. After surgery, immunohistochemistry and fluorescence in situ hybridization (FISH) revealed EWSR1-WT1 gene rearrangement at 22q12, confirming the diagnosis of desmoplastic small round cell tumor. Conclusion: Being different from the predilection of DSRCT for young men, the patient in our case is a 65-year-old man with a huge mass involving the transverse colon and the bladder.

Insight into ozone profile climatology over northeast China from aircraft measurement and numerical simulation.

Tropospheric ozone is a major pollutant that can harm human health, animals and plants. With a rapid development in Northeast China, ozone pollution has become an increasingly serious environmental challenge. To study the ozone distribution and the potential sources of ozone precursors in Northeast China, we analyzed vertical ozone profiles from the In-service Aircraft for a Global Observing System (IAGOS) in 2012-2014 and provided the climatological vertical structure of tropospheric ozone over Shenyang. The tropospheric ozone generally presents high in hot months, mainly due to the combined effects of the strong solar radiation and high volatile organic compounds emission in summer. While in cold months, the ozone is low because of weak solar radiation and high nitrogen oxides emission. Besides, a low-ozone center exists within lower troposphere in August, which is mainly caused by the East Asian summer monsoon prevailing in summer. To analyze the sources of ozone, typical ozone pollution episodes were studied and the results revealed the different pathways for the enhancement of ozone pollution in Shenyang: regional transport of anthropogenic emissions from North China Plain (NCP), long-range transport from Siberian biomass burning and local photochemical production. Modeling results show that the largest contribution to the surface ozone in Northeast China is local anthropogenic emissions (exceed 90%); the regional transport of NCP anthropogenic emissions contribute more to the pollutants around 2 km, and account for more than 50% pollutants during highly ozone polluted days; through long-range transport, Siberian biomass burning in the spring also have a nonnegligible effect on the near-ground ozone in Northeast China. Overall, this study provides tropospheric ozone climatology and its source attribution in Northeast China, and highlight the great importance of regional transport of anthropogenic and biomass burning emissions in ozone pollution.

ENSO and Southeast Asian biomass burning modulate subtropical trans-Pacific ozone transport.

Trans-Pacific transport of enhanced ozone plumes has been mainly attributed to fossil fuel combustion in Asia in spring, but less attention has been paid to vegetation fires in Asia. Here we show that the El Niño-Southern Oscillation (ENSO)-modulated fires in Southeast Asia, rather than Asian fossil fuel plumes, dominate the interannual variability of springtime trans-Pacific transport of ozone across the entire North Pacific Ocean. During El Niño springs, the intensified fires from both the Indochinese Peninsula and Indonesia, together with large-scale circulation anomalies, result in enhanced ozone plumes that stretch over 15 000 km in both the lower-middle and upper troposphere. This enhancement is also observed in the in situ measurements of ozone concentration, with an almost 10% increase at Mauna Loa Observatory, Hawaii, a unique site to monitor the long-distance transport over the North Pacific. This study reports an unexpectedly strong influence of vegetation fires, linked with climate variability, on global tropospheric chemistry and proves once more how complex the interactions in the climate system are.

Impact of enhanced recovery after surgery on postoperative rehabilitation, inflammation, and immunity in gastric carcinoma patients: a randomized clinical trial.

We determined the effects of enhanced recovery after surgery (ERAS) in patients undergoing radical surgery for gastric carcinoma. Sixty patients undergoing radical gastrectomy for gastric carcinoma in Lishui Hospital between March and October 2016 were randomized to receive either ERAS (30 patients) or conventional care (30 patients, controls). Clinical, economic, and laboratory indices were analyzed. ERAS patients showed faster recovery and shorter postoperative hospital stays than the controls (P<0.05). Some clinical indices (i.e., time to first flatus and defecation, time to removal of drainage tubes, time to resumption of oral feeding, time to postoperative mobilization, and postoperative complications) were significantly better in ERAS patients than in controls. Duration of postoperative infusion was lower in ERAS patients than in controls (P<0.05). In ERAS patients, serum albumin and prealbumin were higher on postoperative day 7, C-reactive protein was lower on postoperative days 3 and 7, and neutrophil count was lower on postoperative day 3 compared to the values in controls (P<0.05 for all). IgM levels were higher in ERAS patients on postoperative days 3 and 7 (P<0.05), while IgG levels were higher on postoperative day 3 (P<0.05). Total T lymphocytes were higher in ERAS patients on postoperative day 3, while helper T cells and CD4+/CD8+ ratio were higher on postoperative days 3 and 7 (P<0.05 for all). In gastric carcinoma patients, ERAS may reduce perioperative inflammation, improve immunity and postoperative nutrition, shorten hospitalization, and enhance rehabilitation.

Stratospheric ozone loss over the Eurasian continent induced by the polar vortex shift.

The Montreal Protocol has succeeded in limiting major ozone-depleting substance emissions, and consequently stratospheric ozone concentrations are expected to recover this century. However, there is a large uncertainty in the rate of regional ozone recovery in the Northern Hemisphere. Here we identify a Eurasia-North America dipole mode in the total column ozone over the Northern Hemisphere, showing negative and positive total column ozone anomaly centres over Eurasia and North America, respectively. The positive trend of this mode explains an enhanced total column ozone decline over the Eurasian continent in the past three decades, which is closely related to the polar vortex shift towards Eurasia. Multiple chemistry-climate-model simulations indicate that the positive Eurasia-North America dipole trend in late winter is likely to continue in the near future. Our findings suggest that the anticipated ozone recovery in late winter will be sensitive not only to the ozone-depleting substance decline but also to the polar vortex changes, and could be substantially delayed in some regions of the Northern Hemisphere extratropics.

GC7 blocks epithelial-mesenchymal transition and reverses hypoxia-induced chemotherapy resistance in hepatocellular carcinoma cells.

Hypoxia is common in solid tumors and results in the activation of hypoxia-response genes. Hypoxia-inducible factor-1α (HIF-1α) is thought to reflect major cellular adaptation to hypoxia and contributes to chemoresistance in various tumors including hepatocellular carcinoma (HCC). N1-guanyl-1,7-diaminoheptane (GC7) is an inhibitor which suppresses the active eukaryotic translation initiation factor 5A-2 (eIF5A2), preventing epithelial-mesenchymal transition (EMT) in chemoresistance. In this study, we investigated the role of GC7 in the therapeutic effect of doxorubicin in hypoxia in HCC. We utilized four types of HCC cell line (Huh7, Hep3B, SNU387 and SNU449) in this study. Western blot and immunofluorescence were used to detect expression of epithelial/mesenchymal markers for EMT evaluation and HIF-1α was knocked down using HIF-1α-siRNA. Hypoxia-induced EMT contributed to doxorubicin chemoresistance in HCC cells. Low concentrations of GC7 sensitized Huh7 and Hep3B to doxorubicin by reversing EMT. Knockdown of HIF-1α attenuated hypoxia-induced EMT and abolished the unique feature of GC7. GC7 enhanced sensitivity to doxorubicin in HCC by reversing hypoxia-induced EMT via the HIF-1α-mediated signaling pathway. We suggest a new method of enhancing cytotoxicity of chemotherapy and improving the long-term survival rate in HCC.

Decadal variability of tropical tropopause temperature and its relationship to the Pacific Decadal Oscillation.

Tropopause temperatures (TPTs) control the amount of stratospheric water vapour, which influences chemistry, radiation and circulation in the stratosphere, and is also an important driver of surface climate. Decadal variability and long-term trends in tropical TPTs as well as stratospheric water vapour are largely unknown. Here, we present for the first time evidence, from reanalysis and state-of-the-art climate model simulations, of a link between decadal variability in tropical TPTs and the Pacific Decadal Oscillation (PDO). The negative phase of the PDO is associated with anomalously cold sea surface temperatures (SSTs) in the tropical east and central Pacific, which enhance the zonal SST gradient across the equatorial Pacific. The latter drives a stronger Walker Circulation and a weaker Hadley Circulation, which leads to less convection and subsequently a warmer tropopause over the central equatorial Pacific. Over the North Pacific, positive sea level pressure anomalies occur, which damp vertical wave propagation into the stratosphere. This in turn slows the Brewer-Dobson circulation, and hence warms the tropical tropopause, enabling more water vapour to enter the stratosphere. The reverse chain of events holds for the positive phase of the PDO. Such ocean-troposphere-stratosphere interactions may provide an important feedback on the Earth's global surface temperature.

Toll-like receptors in hepatocellular carcinoma: potential novel targets for pharmacological intervention.

INTRODUCTION: Toll-like receptors (TLRs) are expressed by a wide variety of cell types including immune cells. They play a crucial role in the inflammatory and host defense response against microorganisms, and triggering TLRs can mediate the activation of innate immunity. Furthermore, research suggests that various TLRs may function differently on different tumor cells. The change in TLR activity may elicit an anti-tumor activity in hepatocellular carcinoma (HCC) cells and may serve as a novel therapeutic target for HCC therapy. AREAS COVERED: This review discusses the role of the TLR family in HCC and the underlying signaling pathway of TLRs as a form of pattern recognition receptor in mediating inflammation and HCC immunity responses. Agonists and antagonists of TLRs, which render TLRs as potential therapeutic targets, activate downstream molecules, subsequently causing HCC cell survival. The proliferation or protection against the development of HCC is also described. EXPERT OPINION: A series of studies have highlighted a crucial role of TLRs in HCC and consider TLR signaling pathways as potential therapeutic targets for HCC. However, the conclusions of these studies are in part paradoxical and controversial. Thus, it is necessary to extend further research to help determine the signaling pathways involved.

Impact of enhanced recovery after surgery on postoperative rehabilitation, inflammation, and immunity in gastric carcinoma patients: a randomized clinical trial

We determined the effects of enhanced recovery after surgery (ERAS) in patients undergoing radical surgery for gastric carcinoma. Sixty patients undergoing radical gastrectomy for gastric carcinoma in Lishui Hospital between March and October 2016 were randomized to receive either ERAS (30 patients) or conventional care (30 patients, controls). Clinical, economic, and laboratory indices were analyzed. ERAS patients showed faster recovery and shorter postoperative hospital stays than the controls (P<0.05). Some clinical indices (i.e., time to first flatus and defecation, time to removal of drainage tubes, time to resumption of oral feeding, time to postoperative mobilization, and postoperative complications) were significantly better in ERAS patients than in controls. Duration of postoperative infusion was lower in ERAS patients than in controls (P<0.05). In ERAS patients, serum albumin and prealbumin were higher on postoperative day 7, C-reactive protein was lower on postoperative days 3 and 7, and neutrophil count was lower on postoperative day 3 compared to the values in controls (P<0.05 for all). IgM levels were higher in ERAS patients on postoperative days 3 and 7 (P<0.05), while IgG levels were higher on postoperative day 3 (P<0.05). Total T lymphocytes were higher in ERAS patients on postoperative day 3, while helper T cells and CD4+/CD8+ ratio were higher on postoperative days 3 and 7 (P<0.05 for all). In gastric carcinoma patients, ERAS may reduce perioperative inflammation, improve immunity and postoperative nutrition, shorten hospitalization, and enhance rehabilitation.