Large herbivore grazing accelerates litter decomposition in terrestrial ecosystems

Plant litter decomposition is critical for carbon and nutrient cycling globally. However, the effect of large herbivore grazing on litter decomposition and its mechanisms remain less explored. Here, 1203 paired observations and 381 independent experiments were analyzed to determine how litter decomposition and nutrient cycling respond to changes in grazing intensity. Grazing significantly increased litter decomposition rate by 14.08 % and litter carbon release by 5.03 %, and this effect was observed in grasslands and croplands but not in forests. The positive grazing effect was also found under sheep and cattle/yak grazing. Moderate grazing advanced the home-field advantage effect but inhibited under heavy grazing for grazed litters. The grazing effect was larger for high quality litter than for low quality litter. Litter decomposition slowed under >10 years heavy grazing but accelerated under moderate grazing. The effects of large herbivore grazing on litter decomposition were jointly influenced by grazing intensity, livestock type, climate condition, decomposition duration, litter quality, and soil properties. Our results demonstrated that large herbivore grazing accelerates litter decomposition globally and emphasized the significance and importance of grazing intensity on litter decomposition, which should be integrated into terrestrial ecosystem models.

Dynamic variation in the aroma characteristics of Rhus chinensis honey at different stages after capping

The ripening characteristics after capping of honey are favourable for improving its quality. However, research on the variation and formation of aroma characteristics of honey in this process is lacking. Therefore, the present study was carried out with different stages of Rhus chinensis honeys (RCHs) after capping and identified 192 volatiles with varying levels of concentration. "Fruity" was the main aroma characteristic of RCHs at different stages after capping, mainly contributed by (E)-β-damascenone. Methyl salicylate might be a potential indicator for differentiating RCHs at different stages after capping. The metabolic pathway analyses revealed that the aroma compounds in RCHs undergo transformation at different stages after capping, which subsequently affects its aroma characteristics formation. This work is the first to study the dynamic changes in honey aroma characteristics after capping from multiple perspectives, and the results are of great significance for understanding the aroma characteristics after capping and quality control of honey.

Directed Evolution of Escherichia coli Nissle 1917 to Utilize Allulose as Sole Carbon Source

Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.

Surgical sensation during caesarean section: a qualitative analysis

BACKGROUND

Caesarean section (CS) is a major abdominal surgery performed usually on a young and healthy population under neuraxial anesthesia with little to no sedation. This creates a distinct surgical experience whereby patients are aware of the surgical process, physical sensations, and their environment. This study aimed to provide an in-depth descriptive assessment of subjective surgical experience during CS under regional anaesthesia. We expected the information gained would enhance our current understanding and better alleviate patient anxiety through informed counselling.

METHODS

This qualitative descriptive study was conducted at a Canadian academic centre. Twenty patients participated in semi-structured interviews within a week of CS, using an interview guide developed for this study. Patient medical records were reviewed to collect demographic and surgical information. Thematic analysis was conducted using an inductive approach to determine common themes.

RESULTS

Nine themes were identified. Five themes were identified in the category of surgical sensation and four themes were identified in the category of peri-operative education.

CONCLUSIONS

Patients commonly experienced pressure and movement sensations at varying intensity, and most did not experience pain. Environmental factors, including sounds and distraction by the newborn, affected perception of surgical sensation. Patients wish to receive pre-operative counselling regarding potential surgical sensations, as well as ongoing communication from their anaesthesiologist. These results can be used to guide informed discussions with patients and direct further investigation in this area.

Aromatic profiles and enantiomeric distributions of volatile compounds during the ripening of Dendropanax dentiger honey

Dendropanax dentiger honey (DDH) is a specialty herbal honey from China. Previous research on DDH has mostly focused on its composition and potential chemical markers, no studies have been conducted on the changes in aroma characteristics and chiral odorants during its maturation. Therefore, the present study aims to address the missing parts. The proportions and total concentrations of 185 volatile compounds identified in different classes varied with DDHs ripening. Fourteen common odor-active compounds were identified by odor activity values (OAVs) and GC-olfactometry (GC-O) analysis. The aroma profiles of DDHs were observed to vary at different ripening stages, although the dominant aroma characteristic was "fruity" aroma, which became more pronounced with increasing maturity. The enantiomeric contents and distributions of 7 volatile enantiomers were related to specific physicochemical indicators and the maturity of DDHs, among which the enantiomers of linalool oxide A may be a potential indicator to identify its maturity. Furthermore, precise quantification and OAVs calculation showed that the enantiomer (2S, 5S)-linalool oxide A presented the highest concentration (8.83-27.39 ng/mL) and only the enantiomer R-linalool (OAVs: 5.56-6.14) was an important contributor to the aroma profiles of DDHs at different stages of maturity. These results provided a new research idea for quality control and identification of DDHs at different maturity stages.

Microglia trigger the structural plasticity of GABAergic neurons in the hippocampal CA1 region of a lipopolysaccharide-induced neuroinflammation model

It is well-established that microglia-mediated neuroinflammatory response involves numerous neuropsychiatric and neurodegenerative diseases. While the role of microglia in excitatory synaptic transmission has been widely investigated, the impact of innate immunity on the structural plasticity of GABAergic inhibitory synapses is not well understood. To investigate this, we established an inflammation model using lipopolysaccharide (LPS) and observed a prolonged microglial response in the hippocampal CA1 region of mice, which was associated with cognitive deficits in the open field test, Y-maze test, and novel object recognition test. Furthermore, we found an increased abundance of GABAergic interneurons and GABAergic synapse formation in the hippocampal CA1 region. The cognitive impairment caused by LPS injection could be reversed by blocking GABA receptor activity with (-)-Bicuculline methiodide. These findings suggest that the upregulation of GABAergic synapses induced by LPS-mediated microglial activation leads to cognitive dysfunction. Additionally, the depletion of microglia by PLX3397 resulted in a decrease in GABAergic interneurons and GABAergic inhibitory synapses, which blocked the cognitive decline induced by LPS. In conclusion, our findings indicate that excessive reinforcement of GABAergic inhibitory synapse formation via microglial activation contributes to LPS-induced cognitive impairment.

NSUN2-mediated M5c methylation of IRF3 mRNA negatively regulates type I interferon responses during various viral infections

5-Methylcytosine (m⁵C) is a widespread post-transcriptional RNA modification and is reported to be involved in manifold cellular responses and biological processes through regulating RNA metabolism. However, its regulatory role in antiviral innate immunity has not yet been elucidated. Here, we report that NSUN2, a typical m⁵C methyltransferase, negatively regulates type I interferon responses during various viral infections, including SARS-CoV-2. NSUN2 specifically mediates m⁵C methylation of IRF3 mRNA and accelerates its degradation, resulting in low levels of IRF3 and downstream IFN-β production. Knockout or knockdown of NSUN2 enhanced type I interferon and downstream ISGs during various viral infection in vitro. And in vivo, the antiviral innate response is more dramatically enhanced in Nsun2^+/- mice than in Nsun2^+/+ mice. The highly m⁵C methylated cytosines in IRF3 mRNA were identified, and their mutation enhanced cellular IRF3 mRNA levels. Moreover, infection with Sendai virus (SeV), vesicular stomatitis virus (VSV), herpes simplex virus 1 (HSV-1), or Zika virus (ZIKV) resulted in a reduction of endogenous NSUN2 levels. Especially, SARS-CoV-2 infection (WT strain and BA.1 omicron variant) also decreased endogenous levels of NSUN2 in COVID-19 patients and K18-hACE2 KI mice, further increasing type I interferon and downstream ISGs. Together, our findings reveal that NSUN2 serves as a negative regulator of interferon response by accelerating the fast turnover of IRF3 mRNA, while endogenous NSUN2 levels decrease during SARS-CoV-2 and various viral infections to boost antiviral responses for effective elimination of viruses.

The effect of colour environments on visual tracking and visual strain during short-term simulation of three gravity states

This study investigated the effects of nine colour environments on visual tracking accuracy and visual strain during normal sitting (SP), -12° head-down bed (HD) and 9.6° head-up tilt bed (HU). In a standard posture change laboratory study, fifty-four participants performed visual tracking tasks in nine colour environments while in the three postures. Visual strain was measured by means of a questionnaire. The results showed that in all colour environments, the -12° head-down bed rest posture significantly affected visual tracking accuracy and visual strain. During the three postures, the participants' visual tracking accuracy in the cyan environment was significantly higher than that in other colour environments, and their visual strain was the lowest. Overall, the study adds to our understanding of how environmental and postural factors impact on visual tracking and visual strain.

SMDB: a Spatial Multimodal Data Browser

Understanding the relationship between fine-scale spatial organization and biological function necessitates a tool that effectively combines spatial positions, morphological information, and spatial transcriptomics (ST) data. We introduce the Spatial Multimodal Data Browser (SMDB, https://www.biosino.org/smdb), a robust visualization web service for interactively exploring ST data. By integrating multimodal data, such as hematoxylin and eosin (H&E) images, gene expression-based molecular clusters, and more, SMDB facilitates the analysis of tissue composition through the dissociation of two-dimensional (2D) sections and the identification of gene expression-profiled boundaries. In a digital three-dimensional (3D) space, SMDB allows researchers to reconstruct morphology visualizations based on manually filtered spots or expand anatomical structures using high-resolution molecular subtypes. To enhance user experience, it offers customizable workspaces for interactive exploration of ST spots in tissues, providing features like smooth zooming, panning, 360-degree rotation in 3D and adjustable spot scaling. SMDB is particularly valuable in neuroscience and spatial histology studies, as it incorporates Allen's mouse brain anatomy atlas for reference in morphological research. This powerful tool provides a comprehensive and efficient solution for examining the intricate relationships between spatial morphology, and biological function in various tissues.

Increased Sparc release from subchondral osteoblasts promotes articular chondrocyte degeneration under estrogen withdrawal

OBJECTIVE

The incidence of osteoarthritis (OA) in menopausal women is significantly higher than in same-aged men. Investigating the role of subchondral osteoblasts in estrogen deficiency-induced OA may help elucidate the pathological mechanism, providing new insights for the diagnosis and treatment of menopausal OA.

METHODS

A classical ovariectomy-induced OA (OVX-OA) rat model was utilized to isolate primary articular chondrocytes and subchondral osteoblasts, which were identified and then cocultured in Transwell. The expression of chondrocyte anabolic and catabolic indicators was evaluated. The differentially expressed proteins in the conditioned medium (CM) of osteoblasts were identified by Liquid Chromatograph-Mass Spectrometer (LC-MS/MS). Normal chondrocytes were treated with osteoblast CM, and then RNA sequencing was performed on the treated chondrocytes. KEGG was used to identify significant enrichment of signaling pathways, and Simple Western was used to verify the expression of related proteins in the signaling pathways.

RESULTS

Coculture of OVX-OA subchondral osteoblasts with chondrocytes significantly downregulated the expression of the anabolic indicators and upregulated the expression of the catabolic indicators in chondrocytes. 1,601 proteins were identified in both normal and OVX osteoblast culture supernatants. Protein-protein interaction network analysis revealed that Sparc was one of the hub proteins. The AMPK/Foxo3a signaling pathway of chondrocytes was downregulated by OVX-OA osteoblasts CM. AICAR, the AMPK agonist, partially reversed the catabolic effect of OVX-OA osteoblasts on chondrocytes.

CONCLUSIONS

Sparc secreted by OVX-OA subchondral osteoblasts can downregulate the AMPK/Foxo3a signaling pathway of chondrocytes, thereby promoting chondrocyte degeneration.

Correlation between oral fluid and blood THC concentration: A systematic review and discussion of policy implications

Cannabis is the second most commonly used impairing substance by drivers, after alcohol. As more countries legalize cannabis, there is concern that cannabis-impaired driving will increase. In many countries, police use roadside devices to test for oral fluid THC (the primary psychotropic component in cannabis) to identify drivers who used cannabis; including in countries with non-zero per se limits for THC in blood. This practice is questioned as previous research demonstrates a poor correlation between oral fluid and blood THC concentrations at the individual level. We conducted a meta-analysis to identify all research that compared oral fluid with blood THC levels. We obtained individual-level data from study authors and analyzed pooled individual-level data to calculate sensitivity and specificity of oral fluid THC (at various cut-off values) to detect blood THC above different concentration limits. Finally, we explored practical implications of using oral fluid THC in an enforcement context. Our review found THC concentrations measured in over 18,000 paired samples of oral fluid and blood. We found a good correlation between the presence of THC in oral fluid and presence of THC in blood (sensitivity = 71.2%, specificity = 97.7%). However oral fluid THC, at commonly used cut-off values, is less sensitive and less specific when used as a biomarker to detect people with blood THC concentrations above commonly used per se limits (such as 5 ng/mL). As such, there will be a large number of "false positive" tests if oral fluid THC testing were used as a biomarker for "illegal" THC concentrations in randomly selected drivers. We argue that the adverse implications of false positive oral fluid THC tests in this context outweigh the possible road safety benefits and we recommend against oral fluid THC screening in randomly selected drivers in countries with non-zero per se limits for blood THC. In contrast, oral fluid THC tests appear to be useful for investigating "high-risk" drivers who come to police attention because of evidence of impairment.

The Effect of Correlated Colour Temperature on Physiological, Emotional and Subjective Satisfaction in the Hygiene Area of a Space Station

The hygiene area is one of the most important facilities in a space station. If its environmental lighting is appropriately designed, it can significantly reduce the psychological pressure on astronauts. This study investigates the effect of correlated colour temperature (CCT) on heart rate, galvanic skin response, emotion and satisfaction in the hygiene area of a space station. Forty subjects participated in experiments in a hygiene area simulator with a controlled lighting environment. The lighting conditions included 2700 K, 3300 K, 3600 K, 5000 K and 6300 K; physiological responses (heart rate, galvanic skin response), as well as emotion and satisfaction, were recorded. The results showed that CCT significantly influenced the participants’ physiological and subjective responses in the space station hygiene area. 6300 K led to the best emotion and satisfaction levels, the highest galvanic skin response and the lowest heart rate. The opposite was true for 2700 K.

Crucial functions of alpha-actinin 2 in the embryonic heart

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): Wellcome Trust; British Heart Foundation

Background/Introduction

Alpha-actinin is an integral protein of the Z-discs in heart and skeletal muscle cells, with important structural and signalling functions.  Missense variants in alpha-actinin can cause inherited conditions, e.g. myopathies and cardiomyopathies. The underlying disease mechanisms are still unknown.

Purpose

In order to study the disease mechanisms of an alpha-actinin missense variant, which is known to cause Hypertrophic Cardiomyopathy in human patients, a mouse model was generated.

Methods

Mice carrying the alpha-actinin missense variant were generated by CRISPR-Cas9 genome editing. The heterozygous adult mice carrying the alpha-actinin variant were characterised by echocardiography and quantitative PCR. Hearts of homozygous embryos were analysed at E15.5 by high-resolution episcopic microscopy (HREM).

Results

Mice carrying a single copy of the missense variant were viable and had normal appearance. Adult heterozygous mice showed no signs of cardiomyopathy on echocardiography. However, mature male mice displayed molecular signs of cardiomyopathy, such as induction of the fetal gene programme at transcript level.

The attempt to generate adult mice homozygous for the variant failed: 9 breeding pairs produced 18 litters with 83 weaned pups, but no homozygous offspring. Embryonic lethality was confirmed and E15.5 was the latest stage homozygous pups were reliably found to be viable. At this timepoint, genotype distribution was within the expected Mendelian ratios.

HREM of the hearts at this stage revealed increased right ventricular chamber size and decreased left atrial size, when compared to wildtype littermates. Membranous ventricular septal defects were observed in 3 out of 8 homozygous hearts. Further these embryos displayed aortic stenosis and dysplasic leaflets of the pulmonary valve.

Conclusions

Heterozygous adult mice only displayed sub-clinical signs of disease. In contrast, the missense variant is embryonic lethal in the homozygous setting and leads to a range of morphological abnormalities in E15.5 hearts. Future work will identify how altered functions of alpha-actinin cause these changes.

Histone methyltransferase Dot1L recruits O-GlcNAc transferase to target chromatin sites to regulate histone O-GlcNAcylation

O-GlcNAc transferase (OGT) is the distinctive enzyme responsible for catalyzing O-GlcNAc addition to the serine or threonine residues of thousands of cytoplasmic and nuclear proteins involved in such basic cellular processes as DNA damage repair, RNA splicing, and transcription preinitiation and initiation complex assembly. However, the molecular mechanism by which OGT regulates gene transcription remains elusive. Using proximity labeling-based mass spectrometry, here, we searched for functional partners of OGT and identified interacting protein Dot1L, a conserved and unique histone methyltransferase known to mediate histone H3 Lys79 methylation, which is required for gene transcription, DNA damage repair, cell proliferation, and embryo development. Although this specific interaction with OGT does not regulate the enzymatic activity of Dot1L, we show that it does facilitate OGT-dependent histone O-GlcNAcylation. Moreover, we demonstrate that OGT associates with Dot1L at transcription start sites and that depleting Dot1L decreases OGT associated with chromatin globally. Notably, we also show that downregulation of Dot1L reduces the levels of histone H2B S112 O-GlcNAcylation and histone H2B K120 ubiquitination in vivo, which are associated with gene transcription regulation. Taken together, these results reveal that O-GlcNAcylation of chromatin is dependent on Dot1L.

ILF3 represses repeat-derived microRNAs targeting RIG-I mediated type I interferon response

MicroRNAs (miRNAs) play important roles in regulated gene expression and miRNA biogenesis is also subject to regulation, together constituting critical regulatory circuitries in numerous physiological and pathological processes. As a dsRNA binding protein, interleukin enhancer binding factor 3 (ILF3) has been implicated as a negative regulator in miRNA biogenesis, but the mechanism and specificity have remained undefined. Here, combining small-RNA-seq and CLIP-seq, we showed that ILF3 directly represses many miRNAs or perhaps other types of small RNAs annotated in both miRBase and MirGeneDB. We demonstrated that ILF3 preferentially binds to A/U-enriched motifs, which tend to lengthen and/or stabilize the stem-loop in pri-miRNAs, thereby effectively competing with the Microprocessor to block miRNA biogenesis. Focusing on the biological function of ILF3-suppressed miR-582-3p, we discovered that this LINE-derived miRNA targets a critical interferon-inducible gene RIG-I for repression, thus establishing a novel ILF3/miR-582/RIG-I axis in the antiviral response.

Advances in Self-Powered Ultraviolet Photodetectors Based on P-N Heterojunction Low-Dimensional Nanostructures

Self-powered ultraviolet (UV) photodetectors have attracted considerable attention in recent years because of their vast applications in the military and civil fields. Among them, self-powered UV photodetectors based on p-n heterojunction low-dimensional nanostructures are a very attractive research field due to combining the advantages of low-dimensional semiconductor nanostructures (such as large specific surface area, excellent carrier transmission channel, and larger photoconductive gain) with the feature of working independently without an external power source. In this review, a selection of recent developments focused on improving the performance of self-powered UV photodetectors based on p-n heterojunction low-dimensional nanostructures from different aspects are summarized. It is expected that more novel, dexterous, and intelligent photodetectors will be developed as soon as possible on the basis of these works.

Colour schemes to reduce stress response in the hygiene area of a space station: A Delphi study

This paper aims to explore colour schemes to reduce stress response in the hygiene area of a space station. We conducted a two-stage exploratory Delphi-study with 30 international experts. It was found that the overall environment, stool-urine collection device, garbage collection interface and negative pressure package interface of the hygiene area most affected astronauts' experience. Remarkably, experts have highest visual requirements for the cleanliness of the overall environment and for stool and urine collection devices in the hygiene area. These tend to have low saturation and low blackness colours, while the garbage collection interface and negative pressure package interface have conspicuity and discernibility visual requirements. It was found that experts tend to choose high saturation and high brightness colours.

Optical properties of natural small molecules and their applications in imaging and nanomedicine

Natural small molecules derived from plants have fascinated scientists for centuries due to their practical applications in various fields, especially in nanomedicine. Some of the natural molecules were found to show intrinsic optical features such as fluorescence emission and photosensitization, which could be beneficial to provide spatial temporal information and help tracking the drugs in biological systems. Much efforts have been devoted to the investigation of optical properties and practical applications of natural molecules. In this review, optical properties of natural small molecules and their applications in fluorescence imaging, and theranostics will be summarized. First, we will introduce natural small molecules with different fluorescence emission, ranging from blue to near infrared emission. Second, imaging applications in biological samples will be covered. Third, we will discuss the applications of theranostic nanomedicines or drug delivering systems containing fluorescent natural molecules acting as imaging agents or photosensitizers. Finally, future perspectives in this field will be discussed.

Yak miR-2285o-3p attenuates hypoxia-induced apoptosis by targeting caspase-3

miRNAs are a class of hairpin‐derived RNAs, 21–24 nucleotides in length, which are involved in a range of biological processes. The bta‐miR‐2285 family has over 40 members spanning the entire bovine genome. We previously found that bta‐miR‐2285o‐3p was highly expressed in yak heart and lung when compared with cattle, which prompted us to investigate its potential function in high‐altitude adaptation of yaks. In this study, we detected wide‐spread high expression of bta‐miR‐2285o‐3p in yak tissues. Further experiments revealed that the protein tyrosine phosphatase receptor type M (PTPRM) gene was the host gene of bta‐miR‐2285o‐3p and that two linked SNPs in bta‐mir‐2285o precursor affected the biogenesis of mature miRNA (bta‐miR‐2285o‐3p). Functional analysis in vitro indicated that bta‐miR‐2285o‐3p attenuated hypoxia‐induced apoptosis by targeting very low‐density lipoprotein receptor (VLDLR), phosphatase and tensin homolog (PTEN) and caspase‐3. Expression level analysis in vivo revealed the high negative Pearson’s correlation between bta‐miR‐2285o‐3p and caspase3 in yak, highlighting the potential important roles of bta‐miR‐2285o‐3p in yak high‐altitude adaptation. Our study provides a typical model for deciphering the function of miRNAs in environmental adaptation.

The SARS-CoV-2 subgenome landscape and its novel regulatory features

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate negative subgenomes (subgenomic RNAs [sgRNAs]) through transcription-regulating sequence (TRS)-dependent template switching, but the global dynamic landscapes of coronaviral subgenomes and regulatory rules remain unclear. Here, using next-generation sequencing (NGS) short-read and Nanopore long-read poly(A) RNA sequencing in two cell types at multiple time points after infection with SARS-CoV-2, we identified hundreds of template switches and constructed the dynamic landscapes of SARS-CoV-2 subgenomes. Interestingly, template switching could occur in a bidirectional manner, with diverse SARS-CoV-2 subgenomes generated from successive template-switching events. The majority of template switches result from RNA-RNA interactions, including seed and compensatory modes, with terminal pairing status as a key determinant. Two TRS-independent template switch modes are also responsible for subgenome biogenesis. Our findings reveal the subgenome landscape of SARS-CoV-2 and its regulatory features, providing a molecular basis for understanding subgenome biogenesis and developing novel anti-viral strategies.

Parsing the microRNA genetics basis regulating skeletal muscle fiber types and meat quality traits in pigs

Muscle fibers are closely related to human diseases and livestock meat quality. However, the genetics basis of microRNAs (miRNAs) in regulating muscle fibers is not completely understood. In this study, we constructed the whole genome-wide miRNA expression profiles of porcine fast-twitch muscle [biceps femoris (Bf)] and slow-twitch muscle [soleus (Sol)], and identified hundreds of miRNAs, including four skeletal muscle-highly expressed miRNAs, ssc-miR-378, ssc-let-7f, ssc-miR-26a, and ssc-miR-27b-3p. Moreover, we identified 63 differentially expressed (DE) miRNAs between biceps femoris vs. soleus, which are the key candidate miRNAs regulating the skeletal muscle fiber types. In addition, we found that the expression of DE ssc-miR-499-5p was significantly correlated to the expression of Myoglobin (r = 0.6872, P < 0.0001) and Myosin heavy chain 7 (MYH7; r = 0.5408, P = 0.0020), and pH_45 min (r = 0.3806, P = 0.0380) and glucose content (r = -0.4382, P = 0.0154); while the expression of DE ssc-miR-499-3p was significantly correlated to the expression of Myoglobin (r = 0.5340, P = 0.0024) and pH_45 min (r = 0.4857, P = 0.0065). Taken together, our data established a sound foundation for further studies on the regulatory mechanisms of miRNAs in skeletal muscle fiber conversion and meat quality traits in livestock, and could provide a genetic explanation of the role of miRNAs in human muscular diseases.

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients. Our results reveal distinct host inflammatory cytokine profiles to SARS-CoV-2 infection in patients, and highlight the association between COVID-19 pathogenesis and excessive cytokine release such as CCL2/MCP-1, CXCL10/IP-10, CCL3/MIP-1A, and CCL4/MIP1B. Furthermore, SARS-CoV-2 induced activation of apoptosis and P53 signalling pathway in lymphocytes may be the cause of patients' lymphopenia. The transcriptome dataset of COVID-19 patients would be a valuable resource for clinical guidance on anti-inflammatory medication and understanding the molecular mechansims of host response.

Effect of salt concentration on microbial communities, physicochemical properties and metabolite profile during spontaneous fermentation of Chinese northeast sauerkraut

AIM

The aim of this study was to study the effects of salt concentrations on the microbial communities, physicochemical properties, metabolome profiles and sensory characteristics during the fermentation of traditional northeast sauerkraut.

METHODS AND RESULTS

Northeast sauerkraut was spontaneously fermented under four salt concentrations (0·5, 1·5, 2·5 and 3·5%, w/w). The result of microbiological analysis showed that the population of lactic acid bacteria in 2·5%-salted sauerkraut was significantly higher than that in the other samples. Correspondingly, the speed of decrease in pH and accumulation of acids were the highest in 2·5%-salted sauerkraut. The glucose (analysed by HPLC) in 2·5%-salted sauerkraut was consumed more completely to produce higher levels of organic acids compared to those in the other samples. Principle component analysis showed clear differences in the metabolites of sauerkraut according to different salt concentrations. A higher level of volatiles (detected by HS-SPME/GC-MS) was identified in 2·5%-salted sauerkraut, and sensory evaluation demonstrated that 2·5%-salted sauerkraut had the best sensory characteristics.

CONCLUSION

The best quality of sauerkraut was obtained from fermented under 2·5% salt concentration.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study facilitated the understanding of the effects of salt on the sauerkraut fermentation and may be useful for developing the quality of sauerkraut.

METTL3 and N6-Methyladenosine Promote Homologous Recombination-Mediated Repair of DSBs by Modulating DNA-RNA Hybrid Accumulation

Double-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired, may lead to genome instability or cell death. Here, we report that, in response to DSBs, the RNA methyltransferase METTL3 is activated by ATM-mediated phosphorylation at S43. Phosphorylated METTL3 is then localized to DNA damage sites, where it methylates the N6 position of adenosine (m6A) in DNA damage-associated RNAs, which recruits the m6A reader protein YTHDC1 for protection. In this way, the METTL3-m6A-YTHDC1 axis modulates accumulation of DNA-RNA hybrids at DSBs sites, which then recruit RAD51 and BRCA1 for homologous recombination (HR)-mediated repair. METTL3-deficient cells display defective HR, accumulation of unrepaired DSBs, and genome instability. Accordingly, depletion of METTL3 significantly enhances the sensitivity of cancer cells and murine xenografts to DNA damage-based therapy. These findings uncover the function of METTL3 and YTHDC1 in HR-mediated DSB repair, which may have implications for cancer therapy.

β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus

Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.

The cross-talk modulation of excited state electron transfer to reduce the false negative background for high fidelity imaging in vivo

In practice, high fidelity fluorescence imaging in vivo faces many issues, for example: (1) the fluorescence background of the probe is bleached by the wide intensity scale of fluorescence microscopy, displaying an inherent false negative background (FNB); and (2) the dosage of the probe has to be increased to achieve sufficient intensity for in vivo imaging, causing a vicious cycle that exacerbates the FNB. Herein, we constructed a fluorophore (F)-electron donor (D)-electron regulator (R) system, and thereby developed a dual modulation strategy for the de novo design of high fidelity probes. Using cross-talk modulation, the probe allows: (1) enhanced ESET (excited state electron transfer) from F to D, which minimizes the inherent FNB based on synergistic PET (photo induced electron transfer); and (2) the inhibition of PET and weakening of ESET from F to D to maximize the reporting intensity to further reduce the FNB, which is additionally enhanced by an overdose of the probe. To test the implementation, we constructed a 7-hydroxy-2-oxo-2H-chromene-3-carbaldehyde (HPC) series of probes, with HPC (F) as the fluorophore, 2-hydrazinylpyridine, which was screened as an electronically adjustable donor (D), and electronic regulators (R). In particular, HPC-7 and HPC-8 provided cell/zebrafish imaging with negligible background even using the rather low fluorescence scale of microscopy (a region for revealing hidden background). Interestingly, with the specificity of HPC for reporting zinc, we achieved probe HPC-5, which possesses both an ultralow inherent FNB and optimal reporting intensity for tissue and in vivo imaging, enabling the in vivo imaging of zinc in mice for the first time. Under this high-fidelity mode, the fluorescence monitoring of zinc ions during the development of liver cancer in mice was successfully performed. We envision that the dual modulation strategy with the F-D-R system could provide a useful concept for the de novo design of practical probes.

Ratiometric two-photon fluorescent probe for in situ imaging of carboxylesterase (CE)-mediated mitochondrial acidification during medication

A probe for imaging of mitochondrial carboxylesterase and pH has been developed for the visualization of carboxylesterase-mediated acidification in hepatoma cells and hepatic tissues during the administration of antipyretic and anti-inflammatory drugs.

[Application of next generation sequencing in congenital sensorineural deafness]

Objective:The next-generation sequencing technology (NGS) was used to perform genetic testing on children diagnosed with sensorineural hearing loss in outpatient clinics.The information on the status and inheritance of disease causing genes in deafness was analyzed to provide a theoretical basis for genetic counseling, prenatal diagnosis, and birth defects prevention.Method:Ninety-four cases of sensorineural deafness diagnosed by medical history, audiological examination, and imaging examination were collected in our department.Next-generation sequencing was used to detect the region of exons of 159 genes, 6 mitochondrial genes, and 3 miRNAs related to deafness. The Sanger sequencing verification was performed on the parents of the probands to find out the gene expression status and relationship between the probands and the parents.Result:Of the 94 children with deafness,70 had severe sensorineural hearing loss, 13 had moderate to severe hearing loss, 8 had moderate hearing loss, and 3 had mild hearing loss.Twenty-three cases of cariogenic mutations were detected by next generation sequencing,and the total mutation rate was 24.5%. There were 11 cases of GJB2 mutations, including 6 homozygous mutations of 235delC, 4 heterozygous mutations of 235delC and 299_300del heterozygous mutation of 235delC and c.176_191del.There are 5 cases of SLC26A4 gene mutations, including 2 cases of homozygous mutations of c.919-2A> G, one case of c.919-2A> G and c.2168A>G compound heterozygous mutations, c.919-2A> G and c.754T> C compound heterozygous mutation in 1 case, c.919 2A> G and c.416-418del complex heterozygous mutation in 1 case. There were 2 cases of MT RNR1 mutations, and 1 case of STRC,KCNQ1,USH2A,POU3F4, and MITF mutations.Conclusion:The next-generation sequencing has features such as rapid, high throughput, and low cost, which is beneficial to medication guidance, genetic counseling, and marriage and parenting guidance,and help to effectively prevent or reduce the occurrence of hereditary deafness..

Protective effects of a composition of Chinese herbs-Gurigumu-13 on retinal ganglion cell apoptosis in DBA/2J glaucoma mouse model

AIM

To explore the concrete mechanism of a Mongolian compound medicine-Gurigumu-13 (GRGM) for glaucoma treatment.

METHODS

DBA/2J mice, as glaucoma models, were intragastric administrated with GRGM to study the effect of GRGM on retinal ganglion cells (RGCs). The loss of RGCs was evaluated with the number of RGCs and axons. The expression of the target protein of RGCs or mouse retinas was determined by Western blot. The relative content of malondialdehyde (MDA) was examined by ELISA assay.

RESULTS

GRGM distinctly improved retina damage via increasing the number of neurons, RGCs and axons in a concentration dependent manner. Meanwhile, GRGM obviously decreased the high level of MDA and the expression of oxidative stress-related proteins in retinas of DBA/2J mice, but promoted the expression of antioxidant proteins. Additionally, GRGM also significantly inhibited the protein expression of Bip and Chop, which were markers of endoplasmic reticulum stress-induced apoptosis.

CONCLUSION

GRGM have obvious protective effects on RGCs in DBA/2J mice, and increase the number of RGCs and axons via inhibiting oxidative stress and endoplasmic reticulum stress.

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice

Galacto-oligosaccharides (GOS) are prebiotics that positively affect the host's gut microbiota, which is important for the health of the host.

[Study on the recent application of ear correction model in children with congenital auricular deformity]

Objective:To study the short-term effect of Earwell ear correction model on congenital auricular deformity in children. Method:Selected 38 children with ear malformation, a total of 42 ears, born at the age of 7 days to 176 days, and the average age was 62.40 days, and all of patients were used the U.S. Earwell correction model for correction. Result:Final auricular morphologic results were classified as excellent (normal shape), good (nearnormal shape), and poor (slight or no improvement). And the patients were divided into group 1 (neonatal period), group 2 (28-90 days) and group 3 (more than 90 days) according to age, after using the Earwell ear correction device, the result which evaluated excellent are 100.00%, 89.47% and 72.73% respectively, and the average correction times are 16.75 days, 26.26 days and 38.91 days respectively, the ratio of complications are 0, 73.68% and 100.00% respectively. Conclusion:The effection of Earwell ear correction model is significant for the correction of children with congenital auricular deformity , the earlier treatment cause the better result, the shorter of the correcting time , and the lower of the complication rate.