Search

Abstract Background Organellar genomes have become increasingly essential for studying genetic diversity, phylogenetics, and evolutionary histories of seaweeds. The order Dictyotales (Dictyotophycidae), a highly diverse lineage within the Phaeophyceae, is long-term characterized by a scarcity of organellar genome datasets compared to orders of the brown algal crown radiation (Fucophycidae). Results We sequenced the organellar genomes of Padina usoehtunii, a representative of the order Dictyotales, to investigate the structural and evolutionary differences by comparing to five other major brown algal orders. Our results confirmed previously reported findings that the rate of structural rearrangements in chloroplast genomes is higher than that in mitochondria, whereas mitochondrial sequences exhibited a higher substitution rate compared to chloroplasts. Such evolutionary patterns contrast with land plants and green algae. The expansion and contraction of the inverted repeat (IR) region in the chloroplast correlated with the changes in the number of boundary genes. Specifically, the size of the IR region influenced the position of the boundary gene rpl21, with complete rpl21 genes found within the IR region in Dictyotales, Sphacelariales and Ectocarpales, while the rpl21 genes in Desmarestiales, Fucales, and Laminariales span both the IR and short single copy (SSC) regions. The absence of the rbcR gene in the Dictyotales may indicate an endosymbiotic transfer from the chloroplast to the nuclear genome. Inversion of the SSC region occurred at least twice in brown algae. Once in a lineage only represented by the Ectocarpales in the present study and once in a lineage only represented by the Fucales. Photosystem genes in the chloroplasts experienced the strongest signature of purifying selection, while ribosomal protein genes in both chloroplasts and mitochondria underwent a potential weak purifying selection. Conclusions Variations in chloroplast genome structure among different brown algal orders are evolutionarily linked to their phylogenetic positions in the Phaeophyceae tree. Chloroplast genomes harbor more structural rearrangements than the mitochondria, despite mitochondrial genes exhibiting faster mutation rates. The position and the change in the number of boundary genes likely shaped the IR regions in the chloroplast, and the produced structural variability is important mechanistically to create gene diversity in brown algal chloroplast.

Abstract Hepatocellular carcinoma (HCC) represents a major global health threat with diverse and complex pathogenesis. Aldo–keto reductase family 1 member B10 (AKR1B10), a tumor-associated enzyme, exhibits abnormal expression in various cancers. However, a comprehensive understanding of AKR1B10's role in HCC is lacking. This study aims to explore the expression characteristics of AKR1B10 in HCC and its correlation with clinicopathological features, survival prognosis, and tumor immune microenvironment, further investigating its role and potential regulatory mechanisms in HCC. This study conducted comprehensive analyses using various bioinformatics tools and databases. Initially, differentially expressed genes related to HCC were identified from the GEO database, and the expression of AKR1B10 in HCC and other cancers was compared using TIMER and GEPIA databases, with validation of its specificity in HCC tissue samples using the HPA database. Furthermore, the relationship of AKR1B10 expression with clinicopathological features (age, gender, tumor size, staging, etc.) of HCC patients was analyzed using the TCGA database's LIHC dataset. The impact of AKR1B10 expression levels on patient prognosis was evaluated using Kaplan–Meier survival analysis and the Cox proportional hazards model. Additionally, the correlation of AKR1B10 expression with tumor biology-related signaling pathways and tumor immune microenvironment was studied using databases like GSEA, Targetscan, and others, identifying microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) that regulate AKR1B10 expression to explore potential regulatory mechanisms. Elevated AKR1B10 expression was significantly associated with gender, primary tumor size, and fibrosis stage in HCC tissues. High AKR1B10 expression indicated poor prognosis and served as an independent predictor for patient outcomes. Detailed mechanism analysis revealed a positive correlation between high AKR1B10 expression, immune cell infiltration, and pro-inflammatory cytokines, suggesting a potential DANCR-miR-216a-5p-AKR1B10 axis regulating the tumor microenvironment and impacting HCC development and prognosis. The heightened expression of AKR1B10 in HCC is not only related to significant clinical-pathological traits but may also influence HCC progression and prognosis by activating key signaling pathways and altering the tumor immune microenvironment. These findings provide new insights into the role of AKR1B10 in HCC pathogenesis and highlight its potential as a biomarker and therapeutic target.

BackgroundThe prognostic value and immune significance of T-cell proliferation regulators (TCRs) in hepatocellular carcinoma (HCC) have not been previously reported. This study aimed to develop a new prognostic model based on TCRs in patients with HCC.MethodThis study used The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) and International Cancer Genome Consortium-Liver Cancer-Riken, Japan (ICGC-LIRI-JP) datasets along with TCRs. Differentially expressed TCRs (DE-TCRs) were identified by intersecting TCRs and differentially expressed genes between HCC and non-cancerous samples. Prognostic genes were determined using Cox regression analysis and were used to construct a risk model for HCC. Kaplan-Meier survival analysis was performed to assess the difference in survival between high-risk and low-risk groups. Receiver operating characteristic curve was used to assess the validity of risk model, as well as for testing in the ICGC-LIRI-JP dataset. Additionally, independent prognostic factors were identified using multivariate Cox regression analysis and proportional hazards assumption, and they were used to construct a nomogram model. TCGA-LIHC dataset was subjected to tumor microenvironment analysis, drug sensitivity analysis, gene set variation analysis, and immune correlation analysis. The prognostic genes were analyzed using consensus clustering analysis, mutation analysis, copy number variation analysis, gene set enrichment analysis, and molecular prediction analysis.ResultsAmong the 18 DE-TCRs, six genes (DCLRE1B, RAN, HOMER1, ADA, CDK1, and IL1RN) could predict the prognosis of HCC. A risk model that can accurately predict HCC prognosis was established based on these genes. An efficient nomogram model was also developed using clinical traits and risk scores. Immune-related analyses revealed that 39 immune checkpoints exhibited differential expression between the high-risk and low-risk groups. The rate of immunotherapy response was low in patients belonging to the high-risk group. Patients with HCC were further divided into cluster 1 and cluster 2 based on prognostic genes. Mutation analysis revealed that HOMER1 and CDK1 harbored missense mutations. DCLRE1B exhibited an increased copy number, whereas RAN exhibited a decreased copy number. The prognostic genes were significantly enriched in tryptophan metabolism pathways.ConclusionsThis bioinformatics analysis identified six TCR genes associated with HCC prognosis that can serve as diagnostic markers and therapeutic targets for HCC.

ABSTRACTShiraia-like fungi, which are rare parasitic fungi found around bamboo, play an important role in traditional medicine. Their main active component, hypocrellin, is widely used in medicine, food, and cosmetics. By comparing strains with different hypocrellin yields, we identified a transcription factor (SbTF) in the hypocrellin biosynthesis pathway. SbTF from high-yielding zzz816 and low-yielding CNUCC C72 differed in its protein structure. Subsequently, SbTF from high-yielding zzz816 was overexpressed in several strains. This stabilised the yield in zzz816 and significantly increased the yield in low-yielding CNUCC C72. Comparing downstream non-essential genes between wild type and SbTF-overexpressing CNUCC C72 showed that SbMNF was significantly up-regulated. Therefore, it was selected for further study. SbMNF overexpression increased the hypocrellin yield in low-yielding CNUCC C72 and altered the composition of compounds in high-yielding CNUCC 1353PR and zzz816. This involved an increased elsinochrome C yield in CNUCC 1353PR and an increased hypocrellin B yield in zzz816 (by 2 and 70.3 times that in the corresponding wild type, respectively). This study is the first to alter hypocrellin synthesis to alter the levels of one bioactive agent compared to another. The results provide new insights regarding genetic modification and will help to optimise fungal fermentation.

Abstract Several studies have reported the effects of DJ-1 gene and miR-199a/b-3p on HCC development. However, whether miR-199a/b-3p regulates HCC progression through a novel compensatory signaling pathway involving DJ-1, Ras, and PI3K/AKT remains unknown. We used (TCGA, HPA, miRWalk and Target scan) databases, cancer and para-tissue HCC patients, dual-luciferase reporter gene analysis, proteomic imprinting, qPCR, cell proliferation, scratch, transport, and flow cytometry to detect the molecular mechanism of DJ-1 and miR-199a/b-3p co-expression in HCC cell lines. Bioinformatics analysis showed that DJ-1 was highly expressed in HCC ((P

Eleven leptonetid species belonging to four genera collected in Jiangxi and Fujian Provinces, China are presented. Ten new species of midget cave spiders from southern China are diagnosed, described, and illustrated: Leptonetela dawu Yao & Liu, sp. nov., L. yuanhaoi Yao & Liu, sp. nov. and L. zuojiashanensis Yao & Liu, sp. nov. from Jiangxi; Longileptoneta guadunensis Yao & Liu, sp. nov., L. huboliao Yao & Liu, sp. nov., L. jiaxiani Yao & Liu, sp. nov., L. letuensis Yao & Liu, sp. nov., L. renzhouensis Yao & Liu, sp. nov., L. tianmenensis Yao & Liu, sp. nov., and Pararana mingxuani Yao & Liu, sp. nov. from Fujian. Furthermore, Falcileptoneta monodactyla (Yin, Wang & Wang, 1984) is recorded from Jiangxi province for the first time. Distributions records are given for all investigated species.

Ocean currents play a role in both facilitating and impeding connectivity of marine organisms’ populations, serving as key drivers and potential barriers. The emergence of Taiwan around five million years ago (Mya) impacted the Kuroshio Current which later shaped the distribution of marine organisms. In this study, we examined how the Kuroshio Current influenced the distribution and population divergence of the marine red alga Dichotomaria elegans (Galaxauraceae, Nemaliales). Through phylogenetic analysis, species delimitation, and morphological comparison of Taiwanese species, we determined its phylogenetic position relative to other species within the D. marginata complex of the genus Dichotomaria. We uncovered the hidden cryptic diversity within the D. marginata complex in Taiwan and proposed the new combinations D. elegans and D. latifolia based on Galaxaura elegans and G. latifolia. Genetic analysis based on three loci (mitochondrial cox2-3 and cox1, and plastid rbcL) from 32 locations across the Philippines, Taiwan, and Japan revealed three allopatric lineages within D. elegans. The first lineage is restricted to the northern Philippines and southern Taiwan, while the second has a broader latitudinal range along the Kuroshio Current. The third lineage is found in southeast Luzon, Philippines, close to the bifurcation of the North Equatorial Current, near the start of the Kuroshio Current. The divergence of the first two lineages during the mid-Pliocene (~3.7 Mya) coincided with the emergence of Taiwan, with the current dynamics accentuating their separation. The Kuroshio Current exhibited a dual impact on the biogeography of D. elegans: promoting the dispersal of the second lineage towards higher latitudes and preventing the first lineage from moving northward. Principal component analysis showed that habitat conditions and morphologies differed between the two D. elegans lineages. This study provides insights into the cryptic diversity of Dichotomaria in Taiwan, as well as the genetic divergence, biogeographical patterns, and ecological associations of D. elegans, highlighting the interplay of island formation and currents shaping the diversification of seaweeds in the Northwest Pacific Ocean.

Three new Otacilia species were collected from Jiangxi Provinces, China during a survey of the spider fauna of the region: Otacilia anfu Liu, sp. nov. (♂♀), O. guanshan Liu, sp. nov. (♂♀), and O. mingyueshan Liu, sp. nov. (♂♀). All species are described and illustrated with photographs and SEM micrographs, and their distribution is also mapped.

Objective Arthroscopic release is effective for patients with shoulder stiffness, but the traditional inside‐out procedure cannot effectively alleviate the mobility of some severe stiff shoulder and even cause itrogenic injuries sometimes. The aim of this study is to evaluate the clinical efficacy and advantages of a modified outside‐in shoulder release approach for severe shoulder stiffness. Methods Included in this retrospective study were 15 patients (five male and 10 female) with severe shoulder stiffness who underwent modified outside‐in shoulder release surgery at our hospital between June 2019 and March 2021. Of them, 10 patients had a primary frozen shoulder and five had secondary shoulder stiffness, involving the right shoulder in six cases and the left shoulder in nine cases. The mean age of the 15 patients was 56.7 (34–69) years. The patients were instructed to exercise passively from second‐day post‐operation and enhance the rehabilitation exercise gradually. All patients received a range of motion (ROM) examination before and after surgery. The American Shoulder and Elbow Surgeon's Score (ASES), Constant Score (CS), and Visual Analog Scale (VAS) score for pain were recorded. All data were tested by normal distribution first and then by paired T test, otherwise by Wilcoxon rank sum test. Results The mean follow‐up period was 18.2 (12–33) months. Compared with the preoperative value, the mean ASES score at the final follow‐up improved from 38.4 ± 7.37 to 88.13 ± 6.33 points; the mean CS score from 43.27 ± 6.71 to 78.74 ± 6.93 points; the mean VAS score from 5.07 ± 1.03 to 0.81 ± 0.83 points; forward flexion from 81.93° ± 11.45° to 156.73° ± 9.12°; abduction from 65.93° ± 16.82° to 144.80° ± 8.83°; neutral external rotation from 13.53° ± 10.38° to 51.20° ± 4.77°; internal rotation from the buttock to waist (L3), all showing a significant difference (P

Abstract Background Minerals have crucial biological functions in metabolism and are primarily obtained through diet. As a result, various dietary patterns can impact blood mineral levels. The aim of this study was to investigate the correlation between dietary patterns and the concentration of calcium, magnesium, iron, zinc, and copper in the bloodstream. Methods Three hundred eighty healthy children (53.7% male) were recruited in a region of Hunan Province in September 2019. We gathered basic information and measured physical proportions, along with completing a food frequency questionnaire (FFQ). Using principal component analysis (PCA), we determined dietary patterns. To analyze mineral levels in the blood, we used flame atomic absorption spectrometry (FAAS). We utilized linear regression models to investigate if certain dietary patterns are related to mineral concentration. Results Three dietary patterns were identified: ‘Vegetables/Nuts,’ ‘Snacks/Beverages,’ and ‘Cereal/Beans.’ Children from high-income families (annual average income > 50,000 yuan) prefer the ‘Vegetables/Nuts’ dietary pattern (P = 0.004). In comparison, those from low-income families (annual average income

Mrk 501 is a prototypical high-synchrotron-peaked blazar and serves as one of the primary targets for the Imaging X-ray Polarimetry Explorer (IXPE). In this study, we report X-ray polarization measurements of Mrk 501 based on six IXPE observations. The detection of X-ray polarization at a confidence level exceeding 99% is achieved in four out of the six observations conducted across the entire energy range (2–8 keV) of IXPE. The maximum polarization degree (Π _X ) is measured to be 15.8% ± 2.8%, accompanied by a polarization angle ( ψ _X ) of 98.°0 ± 5.°1 at a confidence level of 5.6 σ . During the remaining two observations, only an upper limit of Π _X < 12% could be derived at the 99% confidence level. No temporal variability in polarization is observed throughout all six IXPE observations for Mrk 501. A discernible trend of energy-dependent variation in the polarization degree is detected in optical spectropolarimetry; however, no analogous indication is observed in Π _X . The chromatic behavior of Π and the consistent values of ψ across different frequencies from X-ray to radio bands, along with the agreement between ψ and jet position angle, strongly support the interpretation of the energy-stratified model with shock-accelerated particles in the jet of Mrk 501. Additionally, the possibility of the presence of a global helical magnetic field in the jet of Mrk 501 is discussed.

ABSTRACTHepatitis E virus (HEV) is a pathogen of global significance, but the value of HEV-related markers in the diagnosis of hepatitis E remains controversial. Previous studies on hepatitis E profiles have been mainly cross-sectional and conducted among inpatients in large hospitals, and hepatitis E cases have been primarily defined by limited partial markers. In this community-based study, 4,110 active hepatitis cases from a population of nearly 600,000 were followed over 48 months and serial serum samples were collected. Both HEV pathogen (HEV RNA and antigen) and anti-HEV antibody markers were used to determine HEV infection status and the relationship between hepatitis and HEV infection. In total, 98 hepatitis E patients were identified and all available isolates from 58 patients belonged to HEV genotype 4. The mean age of the patients was 58.14 years, with an overwhelming proportion of males (70.4%). Hepatitis E accounted for 22.86% of active hepatitis cases with alanine aminotransferase levels ≥15.0-fold the upper limit of normal, suggesting the need to include HEV in routine testing for these patients. Ninety-two hepatitis E patients were positive for at least 2 of HEV antigen, anti-HEV IgM, and HEV RNA markers at presentation, and 90.22% of them were positive for HEV antigen and anti-HEV IgM. HEV antigen, HEV RNA, and anti-HEV IgM positivity were observed in 89.80%, 82.65%, and 93.88% of hepatitis E patients at presentation, respectively. However, only 57.14% of anti-HEV IgM positivity occurred in hepatitis E patients. These findings will advance our understanding of hepatitis E and improve diagnosis.

Two new species of Spinirta Jin & Zhang, 2020 (Araneae: Corinnidae) from Jiangxi Province, China are described here: S. sanxiandian sp. nov. (♂♀) and S. sishuishan sp. nov. (♂). Detailed descriptions and photographs of the new species are provided.

The power density spectrum (PDS) is a powerful tool to study light curves of gamma-ray bursts (GRBs). We show the average PDS and individual PDS analysis with GRB data from the Hard X-ray Modulation Telescope (also named Insight-HXMT). The values of the power-law index of the average PDS ( ${\alpha }_{\bar{P}}$ ) for long GRBs (LGRBs) vary from 1.58 to 1.29 (for 100–245, 245–600, and 600–2000 keV). The Insight-HXMT data allow us to extend the energy of the LGRBs up to 2000 keV, and a relation between ${\alpha }_{\bar{P}}$ and energy E is obtained: ${\alpha }_{\bar{P}}\propto {E}^{-0.09}$ (8–2000 keV). We first systematically investigate the average PDS and individual PDSs for short GRBs (SGRBs), and obtain ${\alpha }_{\bar{P}}\propto {E}^{-0.07}$ (8–1000 keV), where the values of ${\alpha }_{\bar{P}}$ vary from 1.86 to 1.34. The distribution of the power-law index of an individual PDS ( α ) of an SGRB is consistent with that of an LGRB, and the α value for the group with a dominant timescale (the bent power law) is higher than that for the group with no dominant timescale (the single power law). Both LGRBs and SGRBs show similar α and ${\alpha }_{\bar{P}}$ , which indicates that they may be the result of similar stochastic processes. Typical values of the dominant timescale τ for LGRBs and SGRBs are 1.58 s and 0.02 s, respectively. It seems that τ varies in proportion to the duration of GRBs T _90 , with a relation $\tau \propto {T}_{90}^{0.86}$ . The GRB light curve may result from superposing a number of pulses with different timescales. No periodic or quasi-periodic signal above the 3 σ significance threshold is found in our sample.

The afterglows of gamma-ray bursts are believed to have originated from a relativistic jet, which is driven by the merger of compact binary objects or the core collapse of massive stars. Some of their jets may consist of two components: a faster (but narrower) jet and a slower (but wider) jet. The light curves produced by the interaction between the two-component jet and the surrounding medium typically exhibit a chromatic break in multiple bands. For GRB 191221B, the optical light curve of the afterglow exhibits a plateau from 33 to 143 s, followed by a steeper decay that is consistent with the characteristics of reverse shock from an arbitrarily magnetized ejecta. The flattening at ∼10 ks exhibits chromaticity relative to the X-ray afterglow. We propose that the two-component jet scenario can explain this observational result: For the X-ray afterglow, the narrow jet forward shock is dominated until ∼10 ks, and then both the narrow and wide components contribute comparable flux from the forward shock. For the optical afterglow, the first 2 ks is dominated by the narrow jet reverse shock emission (the plateau from 33 to 143 s is due to the jet being magnetized). Between 2 and 10 ks, the forward shock of the narrow jet dominates the optical afterglow, then transitions to wide component forward shock dominance, causing a chromatic plateau. For radio afterglow, the data are only presented after 10 ^5 s, which is dominated by the wide jet forward shock emission.

We present photometric and spectroscopic observations and analysis of the Type IIb supernova (SN) SN 2019tua, which exhibits multiple bumps in its declining light curves between 40 and 65 days after discovery. SN 2019tua shows a time to peak of about 25 days, similar to other Type IIb SNe. Our observations indicate a decrease in its brightness of about 1 mag in the 60 days after the peak. At about days 50 and 60, its multiband light curves exhibit bumpy behavior. The complex luminosity evolution of SN 2019tua could not be well modeled with a single currently popular energy source model, e.g., radioactive decay of ^56 Ni, magnetar, interaction between the ejecta and a circumstellar shell. Even though the magnetar model has a smaller χ ^2 /dof value, the complex changes in SN 2019tua’s brightness suggest that more than one physical process might be involved. We propose a hybrid circumstellar medium (CSM) interaction plus ^56 Ni model to explain the bolometric light curve of SN 2019tua. The fitting results show that the ejecta mass M _ej ≈ 2.4 M _⊙ , the total CSM mass M _CSM ≈ 1.0 M _⊙ , and the ^56 Ni mass M _Ni ≈ 0.4 M _⊙ . The total kinetic energy of the ejecta is E _k ≈ 0.5 × 10 ^51 erg. Preexisting multiple shells suggest that the progenitor of SN 2019tua experienced mass ejections within approximately ∼6–44 yr prior to the explosion.

We present early-time ground-based optical follow-up observations of GRB 180418A, which was discovered by both Swift/BAT and Fermi/GBM. Its broadband afterglow was well monitored by Swift/XRT and ground-based optical telescopes. The optical light curve of GRB 180418A can be modeled by forward shock (FS) plus reverse shock (RS). We fit the light curves with standard external shock models and derive the physical properties of the outflow. It is found that the ratio R _B ≡ ε _B _, _r / ε _B _, _f is 11.22, indicating a moderate degree of magnetization in the RS region. The reported duration of GRB 180418A, T _90 , lies in the intermediate region between short and long gamma-ray bursts (GRBs). We further discuss the classification of GRB 180418A, and calculate ε = E _γ _,iso,52 / E _p _, _z _,2 values of 0.026 and 0.018 (assuming the redshift z is 1.0 and 1.5, respectively), which is closer to short GRBs (SGRBs) in the ε - T _90, _z plane. If GRB 180418A is an SGRB, it is the only reported SGRB thus far with RS emission in optical light curves. In order to compare the properties of GRB 180418A, we collected three SGRBs that may have RS emission (GRBs 060313, 090426, and 210207B) and also 22 long GRBs (LGRBs) with RS emission. We find that the parameters of LGRBs are in a wider range than those of SGRBs. Also, SGRBs appear to have very small R _B values, but the results are generally similar to those of LGRBs. The fitting parameters of GRB 180418A are generally consistent with those of the other three SGRBs, implying that GRB 180418A may belong to the category of SGRBs.