A map of the spatial distribution and tumour-associated macrophage states in glioblastoma and grade 4 IDH-mutant astrocytoma.

Tumour-associated macrophages (TAMs) abundantly infiltrate high-grade gliomas and orchestrate immune response, but their diversity in isocitrate dehydrogenase (IDH)-differential grade 4 gliomas remains largely unknown. This study aimed to dissect the transcriptional states, spatial distribution, and clinicopathological significance of distinct monocyte-derived TAM (Mo-TAM) and microglia-derived TAM (Mg-TAM) clusters across glioblastoma-IDH-wild type and astrocytoma-IDH-mutant-grade 4 (Astro-IDH-mut-G4). Single-cell RNA sequencing was performed on four cases of human glioblastoma and three cases of Astro-IDH-mut-G4. Cell clustering, single-cell regulatory network inference, and gene set enrichment analysis were performed to characterize the functional states of myeloid clusters. The spatial distribution of TAM subsets was determined in human glioma tissues using multiplex immunostaining. The prognostic value of different TAM-cluster specific gene sets was evaluated in the TCGA glioma cohort. Profiling and unbiased clustering of 24,227 myeloid cells from glioblastoma and Astro-IDH-mut-G4 identified nine myeloid cell clusters including monocytes, six Mo/Mg-TAM subsets, dendritic cells, and proliferative myeloid clusters. Different Mo/Mg-TAM clusters manifest functional and transcriptional diversity controlled by specific regulons. Multiplex immunostaining of subset-specific markers identified spatial enrichment of distinct TAM clusters at peri-vascular/necrotic areas in tumour parenchyma or at the tumour-brain interface. Glioblastoma harboured a substantially higher number of monocytes and Mo-TAM-inflammatory clusters, whereas Astro-IDH-mut-G4 had a higher proportion of TAM subsets mediating antigen presentation. Glioblastomas with a higher proportion of monocytes exhibited a mesenchymal signature, increased angiogenesis, and worse patient outcome. Our findings provide insight into myeloid cell diversity and its clinical relevance in IDH-differential grade 4 gliomas, and may serve as a resource for immunotherapy development. © 2022 The Pathological Society of Great Britain and Ireland.

High levels of TIMP1 are associated with increased extracellular matrix stiffness in isocitrate dehydrogenase 1-wild type gliomas.

Glioma progression is accompanied with increased tumor tissue stiffness, yet the underlying mechanisms are unclear. Herein, we employed atomic force microscopy analysis to show that tissue stiffness was higher in isocitrate dehydrogenase (IDH)-wild type gliomas than IDH-mutant gliomas. Bioinformatic analyses revealed that tissue inhibitor of metalloproteinase-1 (TIMP1) was one of the preferentially upregulated genes in IDH-wild type gliomas as compared to IDH-mutant gliomas, and its higher expression indicated worse prognosis of glioma patients. TIMP1 intensity determined by immunofluorescence staining on glioma tissues positively correlated with glioma tissue stiffness. Mechanistically, TIMP1 expression was positively correlated with the gene expression of two predominant extracellular matrix components, tenascin C and fibronectin, both of which were also highly expressed in IDH-wild type gliomas. By introducing IDH1-R132H-containing vectors into human IDH1-wild type glioma cells to obtain an IDH1-mutant cell line, we found that IDH1 mutation increased the TIMP1 promoter methylation through methylation-specific PCR. More importantly, IDH1-R132H mutation decreased both the expression of TIMP1, fibronectin, tenascin C, and the tumor tissue stiffness in IDH1-mutant glioma xenografts in contrast to IDH1-wild type counterparts. Moreover, TIMP1 knockdown in IDH-wild type glioma cells inhibited the expression of tenascin C and fibronectin, and decreased tissue stiffness in intracranial glioma xenografts. Conclusively, we revealed an IDH mutation status-mediated mechanism in regulating glioma tissue stiffness through modulating TIMP1 and downstream extracellular matrix components.

Overexpression of carnitine palmitoyltransferase 1A promotes mitochondrial fusion and differentiation of glioblastoma stem cells.

Glioma stem cells (GSCs) are self-renewing tumor cells with multi-lineage differentiation potential and the capacity of construct glioblastoma (GBM) heterogenicity. Mitochondrial morphology is associated with the metabolic plasticity of GBM cells. Previous studies have revealed distinct mitochondrial morphologies and metabolic phenotypes between GSCs and non-stem tumor cells (NSTCs), whereas the molecules regulating mitochondrial dynamics in GBM cells are largely unknown. Herein, we report that carnitine palmitoyltransferase 1A (CPT1A) is preferentially expressed in NSTCs, and governs mitochondrial dynamics and GSC differentiation. Expressions of CPT1A and GSC marker CD133 were mutually exclusive in human GBMs. Overexpression of CPT1A inhibited GSC self-renewal but promoted mitochondrial fusion. In contrast, disruption of CPT1A in NSTCs promoted mitochondrial fission and reprogrammed NSTCs toward GSC feature. Mechanistically, CPT1A overexpression increased the phosphorylation of dynamin-related protein 1 at Ser-637 to promote mitochondrial fusion. In vivo, CPT1A overexpression decreased the percentage of GSCs, impaired GSC-derived xenograft growth and prolonged tumor-bearing mice survival. Our work identified CPT1A as a critical regulator of mitochondrial dynamics and GSC differentiation, indicating that CPT1A could be developed as a molecular target for GBM cell-differentiation strategy.

The life cycle and development characteristics of Dermacentor everestianus (Acari: Ixodidae) under field conditions in Qinghai-Tibet Plateau.

The tick Dermacentor everestianus mainly distributed in Tibet, China and Nepal, and can transmit some pathogens causing great damages in Qinghai-Tibet Plateau. This study investigated the life cycle and development characteristics of D. everestianus under field conditions. The average duration of the whole life cycle of D. everestianus was 124.4 days, with the host available in the field plot. Under natural conditions, the mean feeding, preoviposition and oviposition period of female ticks were 6.1, 17.9 and 21.2 days, respectively. The incubation time of eggs was the longest phase in the life cycle of the ticks (26 days on average). Moreover, the weight of engorged females was highly positively correlated with the number of the eggs that were laid (r = 0.81, P < 0.05). The reproductive efficiency index and reproductive fitness index in females were 7.3 and 5.9, respectively. The above findings suggest that the tick D. everestianus have evolved well adaptability to the highland areas.

Androgenesis, gynogenesis, and parthenogenesis haploids in cucurbit species.

Haploids and doubled haploids are critical components of plant breeding. This review is focused on studies on haploids and double haploids inducted in cucurbits through in vitro pollination with irradiated pollen, unfertilized ovule/ovary culture, and anther/microspore culture during the last 30 years, as well as comprehensive analysis of the main factors of each process and comparison between chromosome doubling and ploidy identification methods, with special focus on the application of double haploids in plant breeding and genetics. This review identifies existing problems affecting the efficiency of androgenesis, gynogenesis, and parthenogenesis in cucurbit species. Donor plant genotypes and surrounding environments, developmental stages of explants, culture media, stress factors, and chromosome doubling and ploidy identification are compared at length and discussed as methodologies and protocols for androgenesis, gynogenesis, and parthenogenesis in haploid and double haploid production technologies.

[Risk assessment of different grades of hypertension during the treatment of patients with acute pulpitis].

OBJECTIVE: To evaluate the vital signs changes, influence factors in different grades of hypertension patients during the treatment of acute pulpitis, in order to obtain the risk prevention measures. METHODS: In this study, 90 different grades of hypertension patients with acute pulpitis were recruited from February 2014 to February 2015 in the Department of Oral Emergency, Peking University School and Hospital of Stomatology. The information about the patients'general health, oral treatment, life signs of change information was collected. Patients were divided into high risk group, middle risk group, and low risk group (30 patients for each group). RESULTS: (1) Compared with the preoperative, systolic blood pressure (90%), diastolic blood pressure (80%), heart rate increase (100%) were increased in the high risk group. The increase rates of the middle risk group and the low risk group were significantly lower than those of the high risk group (P<0.01). At the same time, the systolic blood pressure of 1/4 (26.7%) patients in high risk group increased more than 20 mmHg (1 mmHg=0.133 kPa), and the diastolic blood pressure of 2/5 patients in high risk group increased more than 10 mmHg, the difference was statistically significant compared with the other two groups (P<0.05). (2) Compared with the preoperative, the average increase of the maximum peak were increased [systolic blood pressure (18.0 ± 1.5) mmHg, diastolic blood pressure (8.0 ± 1.7) mmHg], the mean of heart rate changes [(7.0 ± 0.3) beats per minute] was also increased in the high risk group, while these two indicators were decreased in the low risk group and the middle risk group. The electrocardiogram (ECG) was changed in 6 cases during the treatment in the high risk group. No significantly changed were observed in the low risk group and the middle risk group. (3) Compared the risk assessment in preoperative with that in postoperative, in the middle risk group, 23 cases were evaluated as medium risk in final evaluation, 6 as low risk, and 1 as high risk (risk assessment increased); in the high risk group, 20 cases were evaluated as high risk, 7 as very high risk, and 3 as medium risk (risk assessment decreased). CONCLUSION: Oral treatment is very safe for patients with hypertension, but the risk factor, target organ damage, and complications will also increase the risk of cardiovascular events in elderly patients during the acute pulpitis treatment. Dentist should take some measures to avoid the risks.

Modified shock index is a predictor for 7-day outcomes in patients with STEMI.

SUBJECT: The aim of this study was to compare the predictive values of modified shock index (MSI) and shock index (SI) for 7-day outcome in patients with ST-segment elevation myocardial infarction (STEMI). METHODS: This retrospective study included 160 consecutive patients with STEMI and emergency percutaneous coronary intervention. The blood pressure (BP) and heart rate (HR) measured at emergency department were used to calculate SI (HR/systolic BP) and MSI (HR/mean artery pressure). The major adverse cardiac events (MACE) included all-cause mortality, life-threatening arrhythmias, cardiogenic shock, and Killip class within 7 days. RESULTS: Forty-nine patients had increased MSI (≥1.4), whereas 72 had increased SI (≥0.7). Except the parameters on BP and HR, other parameters were similar between the normal and increased SI groups. However, the increased MSI group had significantly higher age (69.0 ± 13.0 years vs 63.9 ± 12.9 years, P = .025) than the normal MSI group. The 7-day all-cause mortality was 8.8%, and MACE rate was 24.4% in this study. Both increased SI and increased MSI predicted higher MACE rates. However, the odds ratios of increased MSI for all-cause mortality (6.8 vs 3.4), cardiogenic shock (3.0 vs 1.6), life-threatening arrhythmias (9.1 vs 4.6), and MACE (6.8 vs 3.4) were higher than those of increased SI. Modified shock index and SI were independent factor for MACE, but the odds ratio of MSI was higher than of SI (3.05 vs 1.07). CONCLUSIONS: Both SI and MSI in emergency department could predict the all-cause mortality and MACE rates within 7 days in patients with STEMI, but MSI may be more accurate than SI.

High quality repair of osteochondral defects in rats using the extracellular matrix of antler stem cells.

BACKGROUND: Cartilage defects are some of the most common causes of arthritis. Cartilage lesions caused by inflammation, trauma or degenerative disease normally result in osteochondral defects. Previous studies have shown that decellularized extracellular matrix (ECM) derived from autologous, allogenic, or xenogeneic mesenchymal stromal cells (MSCs) can effectively restore osteochondral integrity. AIM: To determine whether the decellularized ECM of antler reserve mesenchymal cells (RMCs), a xenogeneic material from antler stem cells, is superior to the currently available treatments for osteochondral defects. METHODS: We isolated the RMCs from a 60-d-old sika deer antler and cultured them in vitro to 70% confluence; 50 mg/mL L-ascorbic acid was then added to the medium to stimulate ECM deposition. Decellularized sheets of adipocyte-derived MSCs (aMSCs) and antlerogenic periosteal cells (another type of antler stem cells) were used as the controls. Three weeks after ascorbic acid stimulation, the ECM sheets were harvested and applied to the osteochondral defects in rat knee joints. RESULTS: The defects were successfully repaired by applying the ECM-sheets. The highest quality of repair was achieved in the RMC-ECM group both in vitro (including cell attachment and proliferation), and in vivo (including the simultaneous regeneration of well-vascularized subchondral bone and avascular articular hyaline cartilage integrated with surrounding native tissues). Notably, the antler-stem-cell-derived ECM (xenogeneic) performed better than the aMSC-ECM (allogenic), while the ECM of the active antler stem cells was superior to that of the quiescent antler stem cells. CONCLUSION: Decellularized xenogeneic ECM derived from the antler stem cell, particularly the active form (RMC-ECM), can achieve high quality repair/reconstruction of osteochondral defects, suggesting that selection of decellularized ECM for such repair should be focused more on bioactivity rather than kinship.

Intravitreal injection of conbercept for diabetic macular edema complicated with diabetic nephropathy.

AIM: To observe the therapeutic effect of conbercept on diabetic macular edema (DME) complicated with diabetic nephropathy (DN). METHODS: In this retrospective study, 54 patients (54 eyes) that diagnosed as DME from January 2017 to October 2021 were collected. The patients were divided into two groups: DME patients with DN (25 eyes), and DME patients without DN (29 eyes). General conditions were collected before treatment, laboratory tests include fasting blood glucose, HbA1c, microalbumin/creatinine, serum creatinine. Optical coherence tomography (OCT) was used to check the ellipsoidal zone (EZ) and external limiting membrane (ELM) integrity. Central macular thickness (CMT), best corrected visual acuity (BCVA), and retinal hyperreflective foci (HF) as well as numbers of injections were recorded. RESULTS: There were significant differences between fasting blood glucose, HbA1c, serum creatinine, urinary microalbumin/creatinine, and estimated glomerular filtration rate (eGFR) between the two groups (all P<0.05). EZ and ELM continuity in the DME+DN group was worse than that in the DME group (P<0.05). BCVA (logMAR) in the DME group was significantly better than that in the DME+DN group at the same time points during treatment (all P<0.05). CMT and HF values were significantly higher in the DME+DN group than that in the DME group at the all time points (all P<0.05) and significantly decreased in both groups with time during treatment. At 6mo after treatment, the mean number of injections in the DME+DN and DME group was 4.84±0.94 and 3.79±0.86, respectively. CONCLUSION: Conbercept has a significant effect in short-term treatment of DME patients with or without DN, and can significantly ameliorate BCVA, CMT and the number of HF, treatment efficacy of DME patients without DN is better than that of DME patients with DN.

Plastic footprint deteriorates dryland carbon footprint across soil-plant-atmosphere continuum.

Plastic fragments are widely found in the soil profile of terrestrial ecosystems, forming plastic footprint and posing increasing threat to soil functionality and carbon (C) footprint. It is unclear how plastic footprint affects C cycling, and in particularly permanent C sequestration. Integrated field observations (including 13C labelling) were made using polyethylene and polylactic acid plastic fragments (low-, medium- and high-concentrations as intensifying footprint) landfilling in soil, to track C flow along soil-plant-atmosphere continuum (SPAC). The result indicated that increased plastic fragments substantially reduced photosynthetic C assimilation (p < 0.05), regardless of fragment degradability. Besides reducing C sink strength, relative intensity of C emission increased significantly, displaying elevated C source. Moreover, root C fixation declined significantly from 21.95 to 19.2 mg m-2, and simultaneously root length density, root weight density, specific root length and root diameter and surface area were clearly reduced. Similar trends were observed in the two types of plastic fragments (p > 0.05). Particularly, soil aggregate stability was significantly lowered as affected by plastic fragments, which accelerated the decomposition rate of newly sequestered C (p < 0.05). More importantly, net C rhizodeposition declined averagely from 39.77 to 29.41 mg m-2, which directly led to significant decline of permanent C sequestration in soil. Therefore, increasing plastic footprint considerably worsened C footprint regardless of polythene and biodegradable fragments. The findings unveiled the serious effects of plastic residues on permanent C sequestration across SPAC, implying that current C assessment methods clearly overlook plastic footprint and their global impact effects.

Synthesis of 6-(trifluoromethyl)phenanthridines via palladium-catalyzed tandem Suzuki/C-H arylation reactions.

A palladium-catalyzed tandem Suzuki/C-H arylation reaction of N-aryltrifluoroacetimidoyl chlorides with arylboronic acids has been developed. A variety of 6-(trifluoromethyl)phenanthridines were prepared in moderate to excellent yields from N-(2-bromophenyl)trifluoroacetimidoyl chlorides which can be conveniently prepared from 2-bromoaniline derivatives.

[Roles of cytokines in stress-induced depression].

Depression is a very common mental health problem in our modern society. Stress is involved in the provocation of depression. The pathogenesis of depressive disorder is still not well known. The development of neuroendocrine immunology opens a new sight for clarification of mechanism underlying stress-induced depression. Chronic stress activates peripheral and central immune systems accompanied with the release of inflammatory mediators, including cytokines. Activated immune system mediates the process of depression through the interaction with neuron system and neuroendocrine system, including regulating the monoamine neurotransmitter system in synthesis, metabolism and reuptake, inducing the overactivation of hypothalamus-pituitary-adrenal (HPA) axis and its negative feedback regulation, and reducing neurogenesis. This present paper reviews the cytokines mechanisms underlying stress-induced depression.

[Long-term outcomes of the high vaginal uterosacral ligament suspension in treatment of the severe pelvic organ prolapse].

OBJECTIVE: To investigate the long-term objective and subjective outcomes of the transvaginal high uterosacral ligament suspension(HUS) in treatment of severe pelvic organ prolapse (POP) . METHODS: From Jun. 2003 to Mar.2013, 136 patients with severe POP quantitation (POP-Q) stage III-IV underwent transvaginal hysterectomy and HUS operation in the First Affiliated Hospital, General Hospital of People's Liberation Army. And 125 patients (91.9%, 125/136) were followed up at a mean of 5.4 years (range of 4.2-9.2 years) . Anterior colporrhaphy (79.2%, 99/125), posterior colporrhaphy (64.0%, 80/125), the perineorrhaphy (96.0%, 120/125) and tension-free suburethral slings (37.6%, 47/125) were performed concurrently, in which 53 (65%, 53/81) patients with severe cystocele and 5 patients (15%, 5/34) with rectocele were augmented with mesh, respectively. Concurrent operation and complications were studied. The objective success of the operation was defined as the leading vaginal edge above hymen.Subjective results were obtained quality-of-life questionnaires, including pelvic floor distress inventory short form (PFDI-20) and pelvic floor impact questionnaire short form (PFIQ-7). RESULT: The mean interval of following up was (5.4 ± 1.2) years.Four patients presented mild anterior vaginal wall prolapse, and the recurrence rate were 3.2% (4/125), but no reoperation and pessary treatment were needed. Therefore, the subjective and objective satisfaction rate was 94.4% (118/125) and 96.8% (121/125). The mean scores of PFDI-20 and PFIQ-7 at 5 years after the operations were 8, 7, significantly lower than 62, 64 (P < 0.01). There were 3 cases of ureter obstruction. Tension-free vaginal tape was performed on 47 cases with stress urinary incontinence (SUI) as indicated. The symptom of 2 patients was not improved significantly after the operation, but one was improved after 6 months. The rate of denovo SUI was in 2(1.6%, 2/125) patients, but no further treatment was needed. CONCLUSIONS: The transvaginal HUS was then conformed to be a safe, minimal traumatic, highly successful and durable procedure for severe POP, so it is worthy of being popularized for clinical application.

Thickness-dependent release of microplastics and phthalic acid esters from polythene and biodegradable residual films in agricultural soils and its related productivity effects.

It is crucial to elucidate the release rate of microplastics (MPs) and phthalic acid esters (PAEs) in agricultural soil and their effects on crop productivity regarding film types and thicknesses. To address this issue, two-year landfill test was performed using 0.016 mm-thick polyethylene (PEt1) & biodegradable (BIOt1), and 0.01 mm-thin polyethylene (PEt2) & biodegradable (BIOt2) residual films as materials with no landfill as CK. Scanning electron microscopy (SEM) and infrared analyses revealed that two-year landfill caused considerable changes in physical forms and spectral peaks in BIO film, which was more pronounced in thin BIO (36.90 % weight loss). Yet, less changes were presented in the above analyzes in polyethylene (PE) films, and thick films damaged relatively less. MPs number was 86,829.11 n/kg in BIOt1 and 134,912.27 n/kg in BIOt2, equivalent to 2.55 and 3.72 times higher than in PEt1 and PEt2, respectively. This was closely associated with PAEs release, as soil PAEs concentration was substantially lower in PEt1 (17.60 g/kg) and PEt2 (21.43 g/kg) than in BIOt1 and BIOt2 (37.12 g/kg and 49.20 g/kg), respectively. Furthermore, maize productivity parameters were negatively correlated with the amount of MPs and PAEs. BIOt2 and PEt1 had the lowest and highest grain yield, respectively. BIO exhibited greater environmental risk and adverse effects on soil and crop productivity than PE film due to physical degradation and release of PAEs. Thickness-wise comparison exhibited that thin film residues had more adverse effect relative to thick film ones.

Plant biomass mediates the decomposition of polythene film-sourced pollutants in soil through plastisphere bacteria island effect.

The polyethylene (PE) film mulching as a water conservation technology has been widely used in dryland agriculture, yet the long-term mulching has led to increasing accumulation of secondary pollutants in soils. The decomposition of PE film-sourced pollutants is directly associated with the enrichment of specific bacterial communities. We therefore hypothesized that plant biomass may act as an organic media to mediate the pollutant decomposition via reshaping bacterial communities. To validate this hypothesis, plant biomass (dried maize straw and living clover) was embedded at the underlying surface of PE film, to track the changes in the composition and function of bacterial communities in maize field across two years. The results indicated that both dry crop straw and alive clover massively promoted the α-diversity and abundance of dominant bacteria at plastisphere, relative to bulk soil. Bacterial communities tended to be clustered at plastisphere, forming the bacteria islands to enrich pollutant-degrading bacteria, such as Sphingobacterium, Arthrobacter and Paracoccus. As such, plastisphere bacteria islands substantially enhanced the degradation potential of chloroalkene and benzoate (p < 0.05). Simultaneously, bacterial network became stabilized and congregated at plastisphere, and markedly improved the abundance of plastisphere module hubs and connectors bacteria via stochastic process. Particularly, bacterial community composition and plastic film-sourced pollutants metabolism were evidently affected by soil pH, carbon and nitrogen sources that were mainly derived from the embedded biomass. To sum up, plant biomass embedding as a nature-based strategy (NbS) can positively mediate the decomposition of plastic-sourced pollutants through plastisphere bacteria island effects.

Priming effects of nZVI on carbon sequestration and iron uptake are positively mediated by AM fungus in semiarid agricultural soils.

We investigated the priming effect of nanoscale zero-valent iron (nZVI) on carbon sink and iron uptake, and the possible mediation by AMF (arbuscular mycorrhizal fungi, Funneliformis mosseae) in semiarid agricultural soils. Maize seed dressings comprised of three nZVI concentrations of 0, 1, 2 g·kg-1 and was tested with and without AMF inoculation under high and low soil moistures, respectively. The ICP-OES observations indicated that both low dose of nZVI (1 g·kg-1) and high dose of nZVI (2 g·kg-1) significantly increased the iron concentrations in roots (L: 54.5-109.8 %; H: 119.1-245.4 %) and shoots (L: 40.8-78.9 %; H: 81.1-99.4 %). Importantly, the absorption and translocation rate of iron were substantially improved by AMF inoculation under the low-dose nZVI. Yet, the excess nanoparticles as a stress were efficiently relieved by rhizosphere hyphae, and the iron concentration in leaves and stems can maintain as high as about 300 mg·kg-1 while the iron translocation efficiency was reduced. Moreover, next-generation sequencing confirmed that appropriate amount of nZVI clearly improved the rhizosphere colonization of Funneliformis mosseae (p < 0.001) and the development of soil fungal community. Soil observations further showed that the hyphae development and GRSP (glomalin-related soil protein) secretion were significantly promoted (p < 0.05), with the increased R0.25 (< 0.25 mm) by 35.97-41.16 %. As a return, AMF and host plant turned to input more organic matter into soils for microbial growth and Fe uptake, and such interactions became more pronounced under drought stress. In contrast, high dose of nZVI (2 g·kg-1) tended to agglomerate on the surface of hyphae and spores, causing severe deformation and inactivation of AMF symbionts. Therefore, the priming effects of nZVI on carbon sequestration and Fe uptake in agricultural soils were positively mediated by AMF via the feedback loop of the plant-soil-microbe system for enhanced adaptation to global climate change.

Evaluation of Myocilin Variant Protein Structures Modeled by AlphaFold2.

Deep neural network-based programs can be applied to protein structure modeling by inputting amino acid sequences. Here, we aimed to evaluate the AlphaFold2-modeled myocilin wild-type and variant protein structures and compare to the experimentally determined protein structures. Molecular dynamic and ligand binding properties of the experimentally determined and AlphaFold2-modeled protein structures were also analyzed. AlphaFold2-modeled myocilin variant protein structures showed high similarities in overall structure to the experimentally determined mutant protein structures, but the orientations and geometries of amino acid side chains were slightly different. The olfactomedin-like domain of the modeled missense variant protein structures showed fewer folding changes than the nonsense variant when compared to the predicted wild-type protein structure. Differences were also observed in molecular dynamics and ligand binding sites between the AlphaFold2-modeled and experimentally determined structures as well as between the wild-type and variant structures. In summary, the folding of the AlphaFold2-modeled MYOC variant protein structures could be similar to that determined by the experiments but with differences in amino acid side chain orientations and geometries. Careful comparisons with experimentally determined structures are needed before the applications of the in silico modeled variant protein structures.

Microplastics affect soil bacterial community assembly more by their shapes rather than the concentrations.

Polyethylene film mulching is a key technology for soil water retention in dryland agriculture, but the aging of the films can generate a large number of microplastics with different shapes. There exists a widespread misunderstanding that the concentrations of microplastics might be the determinant affecting the diversity and assembly of soil bacterial communities, rather than their shapes. Here, we examined the variations of soil bacteria community composition and functioning under two-year field incubation by four shapes (ball, fiber, fragment and powder) of microplastics along the concentration gradients (0.01%, 0.1% and 1%). Data showed that specific surface area of microplastics was significantly positively correlated with the variations of bacterial community abundance and diversity (r=0.505, p<0.05). The fragment- and fiber-shape microplastics displayed more pronounced interfacial continuity with soil particles and induced greater soil bacterial α-diversity, relative to the powder- and ball-shape ones. Strikingly, microplastic concentrations were not significantly correlated with bacterial community indices (r=0.079, p>0.05). Based on the variations of the ßNTI, bacterial community assembly actually followed both stochastic and deterministic processes, and microplastic shapes significantly modified soil biogeochemical cycle and ecological functions. Therefore, the shapes of microplastics, rather than the concentration, significantly affected soil bacterial community assembly, in association with microplastic-soil-water interfaces.

Thickness effects of polyethylene and biodegradable film residuals on soil properties and dryland maize productivity.

Plastic film residuals are increasingly remaining in cultivated lands. However, it is a critical issue how residual plastic type and thickness affect soil properties and crop yield. To address this issue, in situ landfill was conducted using thick polyethylene (PEt1), thin polyethylene (PEt2), thick biodegradable (BIOt1), thin biodegradable (BIOt2) residues, and CK (control) with no residues landfill in a semiarid maize field. The findings demonstrated that the impact of various treatments on soil characteristics and maize yield varied considerably. Soil water content decreased by 24.82% in PEt1 and 25.43% in PEt2, compared to BIOt1 and BIOt2, respectively. BIOt2 treatment increased soil bulk density by 1.31 g cm-3 and lowered soil porosity by 51.11%, respectively; it also elevated the silt/clay proportion by 49.42% relative to CK. In contrast, microaggregate composition in PEt2 was higher (43.02%). Moreover, BIOt2 lowered soil nitrate (NO3-) and ammonium (NH4+) content. Compared with other treatments, BIOt2 resulted in significantly higher soil total nitrogen (STN) and lower SOC/STN. Finally, BIOt2 exhibited the lowest water use efficiency (WUE) (20.57 kg ha-1 mm-1) and yield (6896 kg ha-1) among all the treatments. Therefore, BIO film residues exhibited detrimental impacts on soil quality and maize productivity compared to PE film ones. Considering film thickness, thin residual films more evidently influenced soil quality and maize productivity than thick film ones.

Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases.

The aim of the study is to establish an online database for predicting protein structures altered in ocular diseases by Alphafold2 and RoseTTAFold algorithms. Totally, 726 genes of multiple ocular diseases were collected for protein structure prediction. Both Alphafold2 and RoseTTAFold algorithms were built locally using the open-source codebases. A dataset with 48 protein structures from Protein Data Bank (PDB) was adopted for algorithm set-up validation. A website was built to match ocular genes with the corresponding predicted tertiary protein structures for each amino acid sequence. The predicted local distance difference test-Cα (pLDDT) and template modeling (TM) scores of the validation protein structure and the selected ocular genes were evaluated. Molecular dynamics and molecular docking simulations were performed to demonstrate the applications of the predicted structures. For the validation dataset, 70.8% of the predicted protein structures showed pLDDT greater than 90. Compared to the PDB structures, 100% of the AlphaFold2-predicted structures and 97.9% of the RoseTTAFold-predicted structure showed TM score greater than 0.5. Totally, 1329 amino acid sequences of 430 ocular disease-related genes have been predicted, of which 75.9% showed pLDDT greater than 70 for the wildtype sequences and 76.1% for the variant sequences. Small molecule docking and molecular dynamics simulations revealed that the predicted protein structures with higher confidence scores showed similar molecular characteristics with the structures from PDB. We have developed an ocular protein structure database (EyeProdb) for ocular disease, which is released for the public and will facilitate the biological investigations and structure-based drug development for ocular diseases. Database URL:  http://eyeprodb.jsiec.org.