The effect on the seasonal dynamics of soil N transformation resulting from biochar application in karst mountains

Nitrogen (N) is frequently a limiting element for primary productivity in karst ecosystems due to its low availability. N mineralization drives N availability and is important for improving N use efficiency in soils. While the use of biochar in agricultural and forest ecosystems has attracted great attention recently, little has been reported on the seasonal dynamics of soil N transformation in karst and its response to biochar application. Therefore, we conducted a pot experiment over 1 year using two types of biochar (rice husk biochar and wood biochar) as soil amendments. The results demonstrated that in the karst mountain region, the soil had the highest content of mineral N (19.41 mg/kg) during summer and the lowest content of mineral nitrogen (3.74 mg/kg) during winter. There was a significant positive correlation (p < 0.01) between soil mineral N content and temperature, and between soil temperature and urease activity. Thus, the higher temperatures during summer enhance soil urease activity, making it easier for soil N mineralization to occur, and increasing soil mineral N content. The soil mineral N content of the CK treatment was 2.61–209.42% higher than the other treatments, indicating that the biochar application reduced the soil mineral N content, which was supported by the negative net N mineralization. This may be due to biochar facilitating the adsorption and immobilization of nitrogen. The soil mineral N content of rice husk biochar was significantly higher than that of woody biochar by 109.55%, indicating that woody biochar would adsorb more N or more readily stimulate N immobilization than rice husk biochar. Furthermore, soil N immobilization (negative net N mineralization) after biochar application varied according to the season. The higher temperatures during summer promoted soil N immobilization more with biochar application. These results are crucial to understanding soil N transformation in karst mountains and guiding effective soil management

Splice variants of DOMINO control Drosophila circadian behavior and pacemaker neuron maintenance.

Circadian clocks control daily rhythms in behavior and physiology. In Drosophila, the small ventral lateral neurons (sLNvs) expressing PIGMENT DISPERSING FACTOR (PDF) are the master pacemaker neurons generating locomotor rhythms. Despite the importance of sLNvs and PDF in circadian behavior, little is known about factors that control sLNvs maintenance and PDF accumulation. Here, we identify the Drosophila SWI2/SNF2 protein DOMINO (DOM) as a key regulator of circadian behavior. Depletion of DOM in circadian neurons eliminates morning anticipatory activity under light dark cycle and impairs behavioral rhythmicity in constant darkness. Interestingly, the two major splice variants of DOM, DOM-A and DOM-B have distinct circadian functions. DOM-A depletion mainly leads to arrhythmic behavior, while DOM-B knockdown lengthens circadian period without affecting the circadian rhythmicity. Both DOM-A and DOM-B bind to the promoter regions of key pacemaker genes period and timeless, and regulate their protein expression. However, we identify that only DOM-A is required for the maintenance of sLNvs and transcription of pdf. Lastly, constitutive activation of PDF-receptor signaling rescued the arrhythmia and period lengthening of DOM downregulation. Taken together, our findings reveal that two splice variants of DOM play distinct roles in circadian rhythms through regulating abundance of pacemaker proteins and sLNvs maintenance

Loss of Prune in Circadian Cells Decreases the Amplitude of the Circadian Locomotor Rhythm in Drosophila

The circadian system, which has a period of about 24 h, is import for organismal health and fitness. The molecular circadian clock consists of feedback loops involving both transcription and translation, and proper function of the circadian system also requires communication among intracellular organelles. As important hubs for signaling in the cell, mitochondria integrate a variety of signals. Mitochondrial dysfunction and disruption of circadian rhythms are observed in neurodegenerative diseases and during aging. However, how mitochondrial dysfunction influences circadian rhythm is largely unknown. Here, we report that Drosophila prune (pn), which localizes to the mitochondrial matrix, most likely affects the function of certain clock neurons.Deletion of pn in flies caused decreased expression of mitochondrial transcription factor TFAM and reductions in levels of mitochondrial DNA, which resulted in mitochondrial dysfunction. Loss of pn decreased the amplitude of circadian rhythms.In addition, we showed that depletion of mtDNA by overexpression of a mitochondrially targeted restriction enzyme mitoXhoI also decreased the robustness of circadian rhythms. Our work demonstrates that pn is important for mitochondrial function thus involved in the regulation of circadian rhythms

α-Glucosidase Inhibitors From the Coral-Associated Fungus Aspergillus terreus

Nine novel butenolide derivatives, including four pairs of enantiomers, named (±)-asperteretones A–D (1a/1b–4a/4b), and a racemate, named asperteretone E (5), were isolated and identified from the coral-associated fungus Aspergillus terreus. All the structures were established based on extensive spectroscopic analyses, including HRESIMS and NMR data. The chiral chromatography analyses allowed the separation of (±)-asperteretones A–D, whose absolute configurations were further confirmed by experimental and calculated electronic circular dichroism (ECD) analysis. Structurally, compounds 2–5 represented the first examples of prenylated γ-butenolides bearing 2-phenyl-3-benzyl-4H-furan-1-one motifs, and their crucial biogenetically related metabolite, compound 1, was uniquely defined by an unexpected cleavage of oxygen bridge between C-1 and C-4. Importantly, (±)-asperteretal D and (4S)-4-decarboxylflavipesolide C were revised to (±)-asperteretones B (2a/2b) and D (4), respectively. Additionally, compounds 1a/1b–4a/4b and 5 were evaluated for the α-glucosidase inhibitory activity, and all these compounds exhibited potent inhibitory potency against α-glucosidase, with IC50 values ranging from 15.7 ± 1.1 to 53.1 ± 1.4 μM, which was much lower than that of the positive control acarbose (IC50 = 154.7 ± 8.1 μM), endowing them as promising leading molecules for the discovery of new α-glucosidase inhibitors for type-2 diabetes mellitus treatment

The Lysine Demethylase dKDM2 Is Non-essential for Viability, but Regulates Circadian Rhythms in Drosophila

Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive depending on specific pathological contexts. However, the role of KDM2 proteins during development remains poorly understood. Unlike vertebrates, Drosophila has only one KDM2 homolog (dKDM2), but its functions in vivo remain elusive due to the complexities of the existing mutant alleles. To address this problem, we have generated two dKdm2 null alleles using the CRISPR/Cas9 technique. These dKdm2 homozygous mutants are fully viable and fertile, with no developmental defects observed under laboratory conditions. However, the dKdm2 null mutant adults display defects in circadian rhythms. Most of the dKdm2 mutants become arrhythmic under constant darkness, while the circadian period of the rhythmic mutant flies is approximately 1 h shorter than the control. Interestingly, lengthened circadian periods are observed when dKDM2 is overexpressed in circadian pacemaker neurons. Taken together, these results demonstrate that dKdm2 is not essential for viability; instead, dKDM2 protein plays important roles in regulating circadian rhythms in Drosophila. Further analyses of the molecular mechanisms of dKDM2 and its orthologs in vertebrates regarding the regulation of circadian rhythms will advance our understanding of the epigenetic regulations of circadian clocks

Automatic Recognition of Laryngoscopic Images Using a Deep-Learning Technique

Objectives/Hypothesis: To develop a deep-learning–based computer-aided diagnosis system for distinguishing laryngeal neoplasms (benign, precancerous lesions, and cancer) and improve the clinician-based accuracy of diagnostic assessments of laryngoscopy findings. Study Design: Retrospective study. Methods: A total of 24,667 laryngoscopy images (normal, vocal nodule, polyps, leukoplakia and malignancy) were collected to develop and test a convolutional neural network (CNN)-based classifier. A comparison between the proposed CNN-based classifier and the clinical visual assessments (CVAs) by 12 otolaryngologists was conducted. Results: In the independent testing dataset, an overall accuracy of 96.24% was achieved; for leukoplakia, benign, malignancy, normal, and vocal nodule, the sensitivity and specificity were 92.8% vs. 98.9%, 97% vs. 99.7%, 89% vs. 99.3%, 99.0% vs. 99.4%, and 97.2% vs. 99.1%, respectively. Furthermore, when compared with CVAs on the randomly selected test dataset, the CNN-based classifier outperformed physicians for most laryngeal conditions, with striking improvements in the ability to distinguish nodules (98% vs. 45%, P <.001), polyps (91% vs. 86%, P <.001), leukoplakia (91% vs. 65%, P <.001), and malignancy (90% vs. 54%, P <.001). Conclusions: The CNN-based classifier can provide a valuable reference for the diagnosis of laryngeal neoplasms during laryngoscopy, especially for distinguishing benign, precancerous, and cancer lesions. Level of Evidence: NA Laryngoscope, 130:E686–E693, 2020

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Transcriptional and post-translational mechanisms that regulate Drosophila circadian rhythms

Circadian rhythms are present in most living organisms with 24-hour cylces in behavioral or physiological processes. Circadian rhythms are generated by the endogenous molecular circadian clock, which relies on the negative transcriptional-translational feedback loop (TTFL). TTFL is a conserved clock regulatory mechanism among different species, which gates many aspects of 24-hour molecular changes from cyclic gene expression to rhythmic protein translocation to time-dependent protein-protein /DNA interactions. Drosophila has been a well-established model organism to study the circadian clock. The first clock mutants were identified in a large-scale Drosophila screen in 1971, which, later on, leads to a series of pioneer discoveries of core clock genes in both mammals and flies. In Drosophila, the TTFL consists of a handful of genes, including Clock (Clk), cycle (cyc), period (per), timeless (tim). CLK and CYC form a heterodimer acting as transcriptional activators, and they bind to the E-box region of downstream genes, such as per and tim to promote their transcription. The encoded PER/TIM proteins translocate to nucleus at late night to repress CLK/CYC activity, thus inhibiting their own transcriptional activity. Aside from the CLK/CYC-dependent regulation on per transcription, we found the transcriptional factor, cAMP Response Element-Binding Protein A (CREBA), also binds to per promotor region. The first half of my dissertation focuses on the underlying mechanism of CREBA on circadian clock regulation. Here, we show that downregulation of the transcription factor CREBA causes behavioral and molecular phenotypes reminiscent of those observed when ATX2 or TYF (RNA binding proteins) were depleted. ATX2 and TYF were previously identified to be involved in per translation by binding to polyA sequence of per mRNA. We also found that CREBA genetically and physically interacts with the ATX2/TYF complex. Interestingly, ATX2 also binds to per promotor but in a CREBA-dependent manner. Consistent with this, we observed that both CREBA and ATX2 regulate circadian period via the 5’ end of the per gene. We therefore propose a model in which CREBA deposits the ATX2/TYF complex on per mRNAs during transcription.The second half of my dissertation focuses on that Suppressor of RAS (SUR-8) regulates PER stability. SUR-8 is expressed within circadian neurons and depletion or overexpression of Sur-8 disrupts circadian rhythms. Further behavioral and immunostaining analysis indicates that PER is the primary target of SUR-8. SUR-8 induces phosphorylation changes of PER to further regulate its stability. PER protein phosphorylation levels are significantly increased in Sur-8 knockdown, accounting for the reduced PER levels in Sur-8 RNAi. The downregulation of protein phosphatase 1 catalytic subunit, PP1-87b, phenocopies Sur-8 knockdown and we further identified SUR-8, PP1-87B, and PER are in a protein complex. Moreover, SUR-8 mediates the interaction between PER and PP1-87B, confirming the role of SUR-8 as a scaffold protein. Interestingly, there is more binding of SUR-8 to PER at night than early morning, suggesting a temporal regulation. Together, our findings demonstrate that SUR-8 links PP1-87B with PER to control PER stability and ultimately, to regulate circadian rhythms