Genome-wide identification of phasiRNAs in Arabidopsis thaliana, and insights into biogenesis, temperature sensitivity, and organ specificity.

The knowledge of biogenesis and target regulation of the phased small interfering RNAs (phasiRNAs) needs continuous update, since the phasiRNA loci are dynamically evolved in plants. Here, hundreds of phasiRNA loci of Arabidopsis thaliana were identified in distinct tissues and under different temperature. In flowers, most of the 24-nt loci are RNA-dependent RNA polymerase 2 (RDR2)-dependent, while the 21-nt loci are RDR6-dependent. Among the RDR-dependent loci, a significant portion is Dicer-like 1-dependent, indicating the involvement of microRNAs in their expression. Besides, two TAS candidates were discovered. Some interesting features of the phasiRNA loci were observed, such as the strong strand bias of phasiRNA generation, and the capacity of one locus for producing phasiRNAs by different increments. Both organ specificity and temperature sensitivity were observed for phasiRNA expression. In leaves, the TAS genes are highly activated under low temperature. Several trans-acting siRNA-target pairs are also temperature-sensitive. In many cases, the phasiRNA expression patterns correlate well with those of the processing signals. Analysis of the rRNA-depleted degradome uncovered several phasiRNA loci to be RNA polymerase II-independent. Our results should advance the understanding on phasiRNA biogenesis and regulation in plants.

Perceptions of Chinese women with a history of gestational diabetes regarding health behaviors and related factors: a directed qualitative content analysis.

BACKGROUND: Gestational diabetes mellitus (GDM) is one of the most common metabolic disorders during pregnancy and is associated with adverse outcomes in both mothers and their children. After delivery, women who experience GDM are also at higher risk of both subsequent GDM and type 2 diabetes mellitus (T2DM) than those who do not. Therefore, healthcare providers and public health practitioners need to develop targeted and effective interventions for GDM. In this study, we aimed to explore the perceptions regarding health behaviors and related factors during the inter-pregnancy period among Chinese women with a history of GDM through the lens of the theory of planned behavior (TPB). METHODS: Between December 2021 and September 2022, 16 pregnant Chinese women with a history of GDM were purposively recruited from a tertiary maternity hospital in Shanghai for face-to-face semi-structured interviews. They were asked questions regarding their health behaviors and related factors. The transcribed data were analyzed using a directed qualitative content analysis method based on the theory of TPB. RESULTS: The health-related behaviors of the women varied substantially. We identified five domains that influenced women's behaviors according to TPB constructs and based on the data collected: behavioral attitude (perceived benefits of healthy behaviors and the relationship between experience and attitude towards the oral glucose tolerance testing); subjective norms (influences of significant others and traditional cultural beliefs); perceived behavior control (knowledge of the disease, multiple-role conflict, the impact of COVID-19, an unfriendly external environment and difficulty adhering to healthy diets), incentive mechanisms (self-reward and external incentives); preferences of professional and institutional support (making full use of social media platform and providing continuous health management). CONCLUSIONS: The health-related behaviors of women with a history of GDM were found to be affected by multiple factors. Healthcare professionals are recommended to provide women with sufficient information regarding the disease and to take advantage of the power of the family and other social support networks to improve women's subjective norms and to promote the adoption of a healthy lifestyle.

Peste Des Petits Ruminants Virus N Protein Is a Critical Proinflammation Factor That Promotes MyD88 and NLRP3 Complex Assembly.

Inflammatory responses play a central role in host defense against invading pathogens. Peste des petits ruminants virus (PPRV) causes highly contagious acute or subacute disease of small ruminants. However, the precise mechanism by which PPRV regulates inflammatory responses remains unknown. Here, we revealed a novel mechanism by which PPRV induces inflammation. Our study showed that PPRV induced the secretion of interleukin 1ß (IL-1ß) by activating the NF-κB signaling pathway and the NLRP3 inflammasome. Moreover, PPRV replication and protein synthesis were essential for NLRP3 inflammasome activation. Importantly, PPRV N protein promoted NF-κB signaling pathway and NLRP3 inflammasome via direct binding of MyD88 and NLPR3, respectively, and induced caspase-1 cleavage and IL-1ß maturation. Biochemically, N protein interacted with MyD88 to potentiate the assembly of MyD88 complex and interacted with NLPR3 to facilitate NLRP3 inflammasome complex assembly by forming an N-NLRP3-ASC ring-like structure, leading to IL-1ß secretion. These findings demonstrate a new function of PPRV N protein as an important proinflammation factor and identify a novel underlying mechanism modulating inflammasome assembly and function induced by PPRV. IMPORTANCE An important part of the innate immune response is the activation of NF-κB signaling pathway and NLPR3 inflammasome, which is induced upon exposure to pathogens. Peste des petits ruminants virus (PPRV) is a highly contagious virus causing fever, stomatitis, and pneumoenteritis in goats by inducing many proinflammatory cytokines. Although the NF-κB signaling pathway and NLRP3 inflammasome play an important role in regulating host immunity and viral infection, the precise mechanism by which PPRV regulates inflammatory responses remains unknown. This study demonstrates that PPRV induces inflammatory responses. Mechanistically, PPRV N protein facilitates the MyD88 complex assembly by directly binding to MyD88 and promotes the NLRP3 inflammasome complex assembly by directly binding to NLRP3 to form ring-like structures of N-NLRP3-ASC. These findings provide insights into the prevention and treatment of PPRV infection.

Electro-optic tunable optical filter based on long-period waveguide grating in lithium niobate on insulator with absorption ribbons.

We propose an electro-optic tunable optical filter based on sidewall long period waveguide grating (LPWG) in lithium niobate on insolator (LNOI). The operation of our proposed filter is based on the mode coupling, filtering, and absorption achieved, respectively, with two corrugated sidewall LPWGs, a tapered waveguide, and two metal ribbons. Our typical fabricated devices achieved a 16.32-dB rejection band and an EO tuning efficiency of ∼0.344 nm/V. Our proposed LPWG and filter are compact and could be integrated with other LNOI waveguide devices to realize more sophisticated functions for on-chip optical signal processing.

Meta-analysis of downregulated E-cadherin as a diagnostic biomarker for cervical cancer.

OBJECTIVE: Downregulation of E-cadherin function or expression has been implicated in the progression of cervical cancer. This meta-analysis of updated publications was performed to assess the association of expression alteration of E-cadherin with disease severity and then to determine the diagnostic accuracy of E-cadherin in discriminating cervical lesions including cervical intraepithelial neoplasia (CIN) grade 1 (CIN1), CIN grade 2 (CIN2), CIN grade 3 (CIN3), and cervical cancer. METHODS: The articles published from inception to January 2021 were searched in PubMed, EBSCO, CNKI, and WanFang Database and then evaluated according to the criteria of meta-analysis. The eligible studies were retrieved and further analyzed. A bivariate mixed effects binary regression model was applied to determine pooled effect estimates. RESULTS: 16 studies with 2436 subjects from 7 countries were eligible for this meta-analysis. When compared with CIN1 control, the pooled odds ratios (ORs) with 95% confidence interval (CI) for the association of E-cadherin positivity with CIN2, CIN3, and cervical cancer were 0.34 (95% CI 0.23-0.51), 0.23 (95% CI 0.10-0.54), and 0.10 (95% CI 0.07-0.14), respectively. The pooled sensitivity and specificity for CIN3 or worse were 0.60 (95% CI 0.48-0.70) and 0.82 (95% CI 0.73-0.88) respectively, with the AUC of 0.78 (95% CI 0.74-0.82). Similar performance was found in CIN2 or worse. CONCLUSION: These findings demonstrated that the loss of E-cadherin protein was associated with worsened cervical lesions. E-cadherin might serve as a promising diagnostic biomarker to facilitate the discrimination of precancerous and cancerous lesions.

The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress.

Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO2 fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.

The In Situ Preparation of Ni-Zn Ferrite Intercalated Expanded Graphite via Thermal Treatment for Improved Radar Attenuation Property.

The composites of expanded graphite (EG) and magnetic particles have good electromagnetic wave attenuation properties in the centimeter band, which is valuable in the field of radar wave interference. In this paper, a novel preparation method of Ni-Zn ferrite intercalated EG (NZF/EG) is provided in order to promote the insertion of Ni-Zn ferrite particles (NZF) into the interlayers of EG. The NZF/EG composite is in situ prepared via thermal treatment of Ni-Zn ferrite precursor intercalated graphite (NZFP/GICs) at 900 °C, where NZFP/GICs is obtained through chemical coprecipitation. The morphology and phase characterization demonstrate the successful cation intercalation and NZF generation in the interlayers of EG. Furthermore, the molecular dynamics simulation shows that the magnetic particles in the EG layers tend to disperse on the EG layers rather than aggregate into larger clusters under the synergy of van der Waals forces, repulsive force, and dragging force. The radar wave attenuation mechanism and performance of NZF/EG with different NZF ratios are analyzed and discussed in the range of 2-18 GHz. The NZF/EG with the NZF ratio at 0.5 shows the best radar wave attenuation ability due to the fact that the dielectric property of the graphite layers is well retained while the area of the heterogeneous interface is increased. Therefore, the as-prepared NZF/EG composites have potential application value in attenuating radar centimeter waves.

The Challenges of Long-Term Transcriptional Gene Silencing by RNA Viruses.

Since the past few decades, the small RNA (sRNA) technologies including small interfering RNA and miRNA have been widely explored for therapeutic development. Classically, these sRNAs target the coding regions of mRNA to exert temporal gene silencing in a post-transcriptional manner. Interestingly, sRNAs targeting gene promoters have been recently described to mediate long-term transcriptional gene silencing (TGS) by epigenetic modifications. This has further harnessed the potential applications in gene therapy. However, efficient delivery is a common hurdle for almost any types of gene therapy approaches. In a recent issue of Trends in Biochemical Sciences, Baltusnikas et al. have proposed to use RNA viruses to deliver sRNA for long-term TGS, suggesting long-term therapy by a single administration approach for various diseases, including chronic, incurable, and fatal illnesses. Being a novel and ambitious gene therapy strategy, we hereby would like to emphasize three major challenges and propose potential solutions.

Bioinformatics-assisted, integrated omics studies on medicinal plants.

The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.

Factors influencing physical inactivity status among chinese pregnant women: a cross-sectional study.

BACKGROUND: Regular prenatal physical activity provides numerous health benefits to both mother and fetus. However, little is known about the physical activity status of pregnant women in China and whether they meet the current guidelines for prenatal physical activity. The aims of the study were to assess physical inactivity status and associated factors among pregnant women in Shanghai, China. METHODS: A cross-sectional study of 1636 pregnant women were recruited at a tertiary obstetrics and gynecology hospital in Shanghai. Maternal sociodemographic characteristics and health information were obtained using structured questionnaires or from the electronic medical records. Physical inactivity status was assessed using the International Physical Activity Questionnaire-Short Form. Factors pertinent to physical inactivity were identified by binary logistic regression and were reported with adjusted odds ratios (ORs) and 95% confidence intervals (CIs). All statistical analyses were performed using the SPSS software package. RESULTS: In total, the prevalence of physical inactivity was 47.5%. Walking was the main form of physical activity and only 2.8% of the pregnant women achieved the goal of at least 150 min of moderate-intensity physical activity weekly. Multivariate logistic regression identified a significant negative association of physical inactivity with personal monthly income (adjusted OR 0.648, 95% CI 0.505-0.831), engagement in regular exercise before pregnancy (adjusted OR 0.575, 95% CI 0.464-0.711) and in the second (adjusted OR 0.534, 95% CI 0.411-0.693) or third (adjusted OR 0.615, 95% CI 0.470-0.806) trimester of pregnancy. Women with nausea or vomiting during pregnancy were more likely to be physically inactive during pregnancy (adjusted OR 1.307, 95% CI 1.002-1.705). CONCLUSION: Physical inactivity is highly prevalent among pregnant women in China. Further efforts should be taken to overcome the barriers to prenatal physical activity and to promote moderate- to vigorous-intensity activities among Chinese pregnant women.

(±)-Involucrasins A and B, two pairs of flavanone enantiomers from Shuteria involucrata and their inhibitory effects on the proliferation of various cancer cell lines.

(±)-Involucrasins A (1) and B (2), two pairs of flavanone enantiomers were isolated from Shuteria involucrata. Structurally, both 1 and 2 are rare representatives of 5-dehydroxy/5-demethoxy 2',3',4'-trisubstituted flavanones. Their structures were elucidated on the basis of comprehensive spectroscopic data analysis and comparison with the literature data. Involucrasin B (2) exhibited moderate anti-proliferative activity against Caco-2, MCF-7, MDA-MB-468, and HCT116 cell lines with IC50 values ranging from 7.9-22.7 µM. Involucrasin A (1) exhibited weak inhibitory activity against Caco-2 and MCF-7 cell lines with IC50 values of 25.8 and 26.5 µM, respectively.

Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae).

BACKGROUND: Bletilla striata is one of the important species belonging to the Bletilla genus of Orchidaceae. Since its extracts have an astringent effect on human tissues, B. striata is widely used for hemostasis and healing. Recently, some other beneficial effects have also been uncovered, such as antioxidation, antiinflammation, antifibrotic, and immunomodulatory activities. As a key step towards a thorough understanding on the medicinal ingredient production in B. striata, deciphering the regulatory codes of the metabolic pathways becomes a major task. RESULTS: In this study, three organs (roots, tubers and leaves) of B. striata were analyzed by integrating transcriptome sequencing and untargeted metabolic profiling data. Five different metabolic pathways, involved in polysaccharide, sterol, flavonoid, terpenoid and alkaloid biosynthesis, were investigated respectively. For each pathway, the expression patterns of the enzyme-coding genes and the accumulation levels of the metabolic intermediates were presented in an organ-specific way. Furthermore, the relationships between enzyme activities and the levels of the related metabolites were partially inferred. Within the biosynthetic pathways of polysaccharides and flavonoids, long-range phytochemical transportation was proposed for certain metabolic intermediates and/or the enzymes. CONCLUSIONS: The data presented by this work could strengthen the molecular basis for further studies on breeding and medicinal uses of B. striata.

Low serum calcium and phosphorus and their clinical performance in detecting COVID-19 patients.

BACKGROUND: This study aimed to evaluate the clinical performance of low serum calcium and phosphorus in discriminative diagnosis of the severity of patients with coronavirus disease 2019 (COVID-19). We conducted a single-center hospital-based study and consecutively recruited 122 suspected and 104 confirmed patients with COVID-19 during January 24 to April 25, 2020. Clinical risk factors of COVID-19 were identified. The discriminative power of low calcium and phosphorus regarding the disease severity was evaluated. Low calcium and low phosphorus are more prevalent in severe or critical COVID-19 patients than moderate COVID-19 patients (odds ratio [OR], 15.07; 95% confidence interval [CI], 1.59-143.18 for calcium; OR, 6.90; 95% CI, 2.43-19.64 for phosphorus). The specificity in detecting the severe or critical patients among COVID-19 patients reached 98.5% (95% CI, 92.0%-99.7%) and 84.8% (95% CI, 74.3%-91.6%) by low calcium and low phosphorus, respectively, albeit with suboptimal sensitivity. Calcium and phosphorus combined with lymphocyte count could obtain the best discriminative performance for the severe COVID-19 patients (area under the curve [AUC] = 0.80), and combined with oxygenation index was promising (AUC = 0.71). Similar discriminative performances of low calcium and low phosphorus were found between suspected and confirmed COVID-19 patient. Low calcium and low phosphorus could indicate the severity of COVID-19 patients, and may be utilized as promising clinical biomarkers for discriminative diagnosis.

Effect of mangrove restoration on sediment properties and bacterial community.

Mangrove reconstruction is an efficient approach for mangrove conservation and restoration. The present study aimed to explore the effects of mangrove reconstruction on sediment properties and bacterial community. The results showed that mangrove restoration greatly promoted sediment fertility, whereas the improvements were more obvious induced by Kandelia obovata when compared to Avicennia marina. In all the samples, the dominant top5 bacterial group were Proteobacteria (48.31-54.52%), Planctomycetes (5.98-8.48%), Bacteroidetes (4.49-11.14%) and Acidobacteria (5.69-8.16%). As for the differences among the groups, the relative abundance of Chloroflexi was higher in the sediments of K. obovata, while Bacteroidetes was more abundant in A. marina group. Furthermore, the two bacterial genera (Rhodoplanes and Novosphingobium) were more dominant in the sediments of K. obovata, while the sediments of A. marina contained higher abundance of Vibrio and Marinobacterium. Besides, bacterial community was highly correlated with mangrove species and sediment property and nutrient status. The results of this study would provide a better understanding of the ecological benefits of mangroves and highlighted the information on biogeochemical processes driven by mangrove restoration and microorganisms.

The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis.

Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.

IL-17A promotes fatty acid uptake through the IL-17A/IL-17RA/p-STAT3/FABP4 axis to fuel ovarian cancer growth in an adipocyte-rich microenvironment.

Pro-inflammatory cytokines are crucial mediators of cancer development, representing potential targets for cancer therapy. The molecular mechanism of a vital pro-inflammatory cytokine, IL-17A, in cancer progression and its potential use in therapy through influencing fatty acid (FA) metabolism, especially FA uptake of cancer cells, remains unknown. In the present study, we used IL-17A and ovarian cancer (OvCa), a representative of both obesity-related and inflammation-related cancers, to explore the interactions among IL-17A, cancer cells and adipocytes (which can provide FAs). We found that in the presence of palmitic acid (PA), IL-17A could directly increase the cellular uptake of PA, leading to the proliferation of OvCa cells via the IL-17A/IL-17RA/p-STAT3/FABP4 axis rather than via CD36. Moreover, in vivo experiments using an orthotopic implantation model in IL-17A-deficient mice demonstrated that endogenous IL-17A could fuel OvCa growth and metastasis with increased expression of FABP4 and p-STAT3. Furthermore, analysis of clinical specimens supported the above findings. Our data not only provide useful insights into the clinical intervention of the growth and metastasis of the tumors (such as OvCa) that are prone to growth and metastasis in an adipocyte-rich microenvironment (ARM) but also provides new insights into the roles of IL-17A in tumor progression and immunomodulatory therapy of OvCa.

Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow.

Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs. The nuclear-localized regulatory mode was also reported for the plant miRNAs. However, evidence is still lacking to show the universality and conservation of the miRNA-mediated regulation in the plant nuclei. Here, we introduced a bioinformatics workflow for genome-wide investigation of miRNA-guided, cleavage-based regulation of the nascent nuclear transcripts. Facilitated by the tool package PmiRNTSA (Plant microRNA-mediated nascent transcript slicing analyzer), plant biologists could perform a comprehensive search for the miRNA slicing sites located within the introns or the exon-intron/intron-exon junctions of the target transcripts, which are supported by degradome sequencing data. The results enable the researchers to examine the co-transcriptional regulatory model of the miRNAs for a specific plant species. Moreover, a case study was performed to search for the slicing sites located within the exon-intron/intron-exon junctions in two model plants. A case study was performed to show the feasibility and reliability of our workflow. Together, we hope that this work could inspire much more innovative research efforts to expand the current understanding of the miRNA action modes in plants.

The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants.

The plant RNA degradome was defined as an aggregate of the RNA fragments degraded from various biochemical pathways, such as RNA turnover, maturation and quality surveillance. In recent years, the degradome sequencing (degradome-seq) libraries became a rich storehouse for researchers to study on RNA processing and regulation. Here, we provided a brief overview of the uses of degradome-seq data in plant RNA biology, especially on non-coding RNA processing and small RNA-guided target cleavages. Some novel applications in RNA research area, such as in vivo mapping of the endoribonucleolytic cleavage sites, identification of conserved motifs at the 5' ends of the uncapped RNA fragments, and searching for the protein-binding regions on the transcripts, were also mentioned. More importantly, we proposed a model for the biologists to deduce the contributions of transcriptional and/or post-transcriptional regulation to gene differential expression based on degradome-seq data. Finally, we hope that the degradome-based analytical methods could be widely applied for the studies on RNA biology in eukaryotes.

Nitrogen dynamics in the mangrove sediments affected by crabs in the intertidal regions.

Crab is an important benthonic animal in mangrove ecosystem, however, the potential function of crabs on nitrogen (N) transformation in mangrove ecosystems is still poorly understood. The present study aimed to explore the potential effect of crab burrows on nitrification/denitrification within the sediments. The results showed that the presence of crab burrows could directly promote soil nitrification, the regions within more crab burrows appeared to possess higher nitrification. Higher AOA and AOB gene copies were also observed in the sediments surrounding crab burrows than those in the sediments without crab burrow. On the contrary, lower nirS copies, a denitrification related gene, were detected in the sediments surrounding crab burrows. In summary, the present study proposed new evidences of nitrification enhancement deriving by crabs, the presence of crabs might be significant in alleviating nitrification inhibition and benefits the growth of mangroves under tidal flooding.

Significance and roles of synonymous codon usage in the evolutionary process of Proteus.

Proteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine-tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.