Multivariate mediation analysis with voxel-based morphometry revealed the neurodegeneration pathways from genetic variants to Alzheimer's Disease.

Neurodegenerative processes are increasingly recognized as potential causative factors in Alzheimer's disease (AD) pathogenesis. While many studies have leveraged mediation analysis models to elucidate the underlying mechanisms linking genetic variants to AD diagnostic outcomes, the majority have predominantly focused on regional brain measure as a mediator, thereby compromising the granularity of the imaging data. In our investigation, using the imaging genetics data from a landmark AD cohort, we contrasted both region-based and voxel-based brain measurements as imaging endophenotypes, and examined their roles in mediating genetic effects on AD outcomes. Our findings underscored that using voxel-based morphometry offers enhanced statistical power. Moreover, we delineated specific mediation pathways between SNP, brain volume, and AD outcomes, shedding light on the intricate relationship among these variables.

Reparative effect of different dietary additives on soybean meal-induced intestinal injury in yellow drum (Nibea albiflora).

Soybean meal (SBM) is an acceptable replacement for unsustainable marine fish meal (FM) in aquaculture. However, we previously reported that high dietary SBM supplementation causes intestinal inflammatory injury in yellow drum (Nibea albiflora). Accordingly, a 4-week SBM-induced enteritis (SBMIE) in yellow drum trial was conducted first, followed by a 4-week additive-supplemented reparative experiment to evaluate the reparative effect of five additives on SBMIE in yellow drum. The control diet comprised 50% FM protein substituted with SBM. The additive-supplemented diet was added with 0.02% curcumin (SBMC), 0.05% berberine (SBM-BBR), 0.5% tea polyphenols (SBM-TPS), 1% taurine (SBM-TAU), or 0.8% glutamine (SBM-GLU) based on the control diet, respectively. The weight gain (WG), specific growth rate (SGR), feed efficiency ratio (FER), and survival rate (SR) of fish fed the additive-supplemented diets were significantly higher than those of fish fed the SBM diet. The WG, SGR, and FER of fish fed the SBMC, SBM-GLU and SBM-TAU diets were significantly higher than those of fish fed other diets. Moreover, fish fed the additive-supplemented diets SBMC and SBM-GLU, exhibited significantly increased intestinal villus height (IVH), intestinal muscular thickness (IMRT), and intestinal mucosal thickness (IMLT) and significantly decreased crypt depth (CD) in comparison with those fed the SBM diets. The relative expression of intestinal tight junction factors (ocln, zo1), cytoskeletal factors (f-actin, arp2/3), and anti-inflammatory cytokines (il10, tgfb) mRNA was remarkably elevated in fish fed additive-supplemented diets than those of fish fed the SBM diet. Whereas, the relative expression of intestinal myosin light chain kinase (mlck) and pro-inflammatory cytokines (il1, il6, tnfa) mRNA was markedly lower in fish fed the additive-supplemented diets. The highest relative expression of intestinal ocln, f-actin, and arp2/3 and the lowest relative expression of intestinal mlck were found in fish fed the SBMC diet. Hence, all five dietary additives effectively repaired the intestinal injury induced by SBM, with curcumin exhibiting the strongest repair effect for SBMIE in yellow drum.

Optimum capture size of Trichiurus japonicus in the East China Sea.

Trichiurus japonicus is an economically valuable species in the East China Sea, whose allowable capture size varies with fishing effort in different years. To clarify the optimum capture size for T. japonicus in the East China Sea, we collected samples and data from T. japonicus targeting fishing gears such as trawls, canvas spreader stow nets and longlines from 2016 to 2020. We estimated growth and mortality parameters using the FiSAT II software, and calculated the size limit standards for capture. The results showed that the inflection point of anal length, the critical anal length and the anal length of one-year-old T. japonicus was 382.84, 397.12, and 216.05 mm, respectively. The anal length of maturity was 230.38 mm, and the minimum capture size (anal length) was 219.23 mm. Based on the yield per recruitment analysis using Beverton-Holt model, the current fishery reference points were under overfishing condition (tc=0.38 a, F=2.11), and the suggested optimum capture size was 364.64 mm. There would be a sharp decline of T. japonicus catches in the East China Sea if the suggested minimum capture size was substantially higher, which might be non-practical for local fishermen. Therefore, we suggested 220 mm as the capture size limit, which was close to the anal length of one-year-old fish and the anal length of maturity.

Label-free proteome quantification and evaluation.

The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.

Excitation of mirror symmetry higher-order rational soliton in modulation stability regimes on continuous wave background.

We study the relationship between the structures of the nonlinear localized waves and the distribution characteristics of the modulation stability regime in a nonlinear fiber with both third-order and fourth-order effects. On the background frequency and background amplitude plane, the modulation stability region consists of two symmetric curves on the left and right and a point on the symmetry axis. We find that the higher-order excitation characteristics are obviously different at different positions in the modulation stability region. Their excitation characteristics are closely related to the modulation instability distribution characteristics of the system. It is shown that asymmetric high-order rational solitons are excited at the left and right stable curves, and the symmetric one is excited at the stable points. Interestingly, the asymmetric higher-order rational solitons on the left and right sides are mirror-symmetrical to each other, which coincides with the symmetry of the modulation instability distribution. These results can deepen our understanding of the relationship between nonlinear excitation and modulation instability and enrich our knowledge about higher-order nonlinear excitations.

[Feeding ecology of Engraulis japonicus based on stomach contents and stable isotope]. / åŸºäºŽèƒƒå«ç‰©åˆ†æžå’Œç¨³å®šåŒä½ç´ æŠ€æœ¯ç ”ç©¶é³€çš„æ‘„é£Ÿç”Ÿæ€.

Engraulis japonicus, an important fishery resource, is a key species in ecosystem trophodynamics studies. In this study, we examined stomach content of E. japonicusby stable isotope analyses, with samples collected from the East China Sea in 2008-2009 and 2020. The aim of this study was to demonstrate their diet composition, diel and ontogenetic changes in feeding habits and trophic level. Results of the stomach content analysis showed that E. japonicus mainly fed on planktonic crustaceans and small fish. The main prey species were Euphausia pacifica [index of relative importance (IRI)=87.6%; frequency(F)=57.6%], Paracalanus parvus (IRI=3.2%, F=15.3%), and Themisto gracilipes (IRI=2.1%, F=13.1%). Results of the stable isotope analysis showed that Copepoda were the main food source of E. japonicus, followed by Euphausiacea, and the contribution rate of Amphipoda was the least, which was less than 1%. There was significant diel change in diet composition. Feeding intensity was higher in the daytime than at night, with the highest in the dusk and the lowest at midnight. Ontogenetic change in feeding habit occurred when fork length reached 90 mm, over which the fish fed both zooplankton and small fishes. The δ13C of E. japonicus was between -21.66‰ and -18.14‰, with an average of (-19.92±0.86)‰. The δ15N of E. japonicus ranged from 4.07‰ to 10.78‰, with an average of (8.14±2.48)‰. Both δ13C and δ15N values were positively correlated with fork length. Trophic level of the fish was 3.4 with stomach content analysis and 2.7 with stable isotope analysis. The results would provide important reference for understanding nutritional status of pelagic small fish, and offer some basic data to establish ecopath model.

[Spatio-temporal niche of dominant shrimp species in the Zhongjieshan Islands Marine Protected Area, China]. / 中街山列岛海洋保护区虾类优势种时空生态位.

To understand the characteristics and living conditions of shrimp population in the Zhongjieshan Islands Marine Protected Area (MPA), according to the trawl survey data of the area in January, April, July and October 2018, we analyzed the spatio-temporal niche of dominant shrimp species based on the indices of relative importance, Shannon index, Pianka formula and Pearson correlation coefficient. The results showed that 16 shrimp species from 10 families and 13 genera were collected and identified. Palaemon gravier, Solenocera crassicorni, Alpheus distinguendus, Parapenaeopsis hardwickii and Alpheus japonicus were dominant species, belonging to four fami-lies and four genera. The temporal niche breadth of the dominant species varied greatly, while their spatial niche breadth was stable. The temporal niche breadth was significantly correlated with temperature suitability. The spatio-temporal niche breadth value of A. japonicus, the small shrimps, was highest. The temporal niche overlap value between P. hardwickii and S. crassicornis was the largest, indicating that the time synchronization was high and the seasonal competition was severe. There was a significant spatial niche overlap in all dominant species, indicating that the dominant species of shrimp had the same spatial homology, with strong regional competition. The spatio-temporal niche overlap value between P. hardwickii and P. gravieri was the largest, indicating that they had high similarities in physical and biological environment selecting, spawning and migratory habits, and fierce inter-specific competition. Our results could provide reference for the application of spatio-temporal niche of marine organisms.

Accumulation and Elimination of Tetrodotoxin in the Pufferfish Takifugu obscurus by Dietary Administration of the Wild Toxic Gastropod Nassarius semiplicata.

To investigate pufferfish accumulation, elimination, and distribution of tetrodotoxin (TTX), Takifugu obscurus was fed with wild TTX-containing gastropod Nassarius semiplicata to simulate the natural food chain. Three-month-old non-poisonous T. obscurus was fed with wild toxic N. semiplicata at three exposure dose for 28 days, and later, with toxin-free food until day 67. Three fish individuals from each treatment were sampled, and the distribution of TTX in different tissues was measured. The results showed that the accumulation ratio of TTX in the three exposure dose groups ranged from 35.76% to 40.20%. The accumulation ratio in the skin and liver was the highest amongst all tissues, accounting for more than 85% of the total TTX, whereas that in the kidney and gallbladder was the lowest (0.11%-0.78%). Studies on the kinetic of TTX accumulation and elimination revealed that the skin was the tissue with the highest accumulation speed constant (8.06), while the liver, kidney, and intestinal tract showed the highest speed of TTX elimination. The time required for TTX reduction to reach the safety limit could be predicted by using standard elimination equations. Qualitative analysis by UPLC-MS/MS revealed the occurrence of seven TTX derivatives in T. obscurus; of these TTX, 5-deoxy TTX, 11-deoxy TTX, 4,9-anhydro TTX were found in all tested tissues.

Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress.

Heat shock proteins 70 (Hsp70) are required for key cellular processes and responses to environmental changes, however, there are an unknown number of hsp70 gene family members in the large yellow croaker (Larimichthys crocea). In the present study, 17 hsp70 genes were identified through the genome of the large yellow croaker. These genes are divided into seven evolutionarily distinct groups according to a phylogenetic tree. The orthologs of these hsp70 genes were found in humans and zebrafish. The expression patterns of the hsp70 gene family in the large yellow croaker under cold and heat stress were studied by examining transcriptome data. Six out of 17 genes were significantly unregulated or downregulated after cold or heat stress. There were two genes significantly upregulated and two genes downregulated in the liver after cold treatment, while after heat treatment, five genes were significantly upregulated, and no genes were significantly downregulated. Three expression patterns were detected: strictly heat-inducible hsp70, constitutively expressed and moderately heat-inducible hsp70, and constitutively expressed and less stress-dependent hsp70 genes. All the findings will contribute to a better understanding of the biological function of hsp70s in defending against thermal challenges.

Phylogeography and population structure of - grypotus (Richardson, 1846) as revealed by mitochondrial control region sequences.

The 137 individuals of Johnius grypotus were collected from seven localities from the Bohai Sea to the East China Sea. A 549 base pair (bp) fragment of the hypervariable region of the mtDNA control region was sequenced to examine genetic diversity and population structure. The populations of J. grypotus showed high haplotype diversity (h) with a range from 0.7500 to 0.9740 and low nucleotide diversity (π) with a range from 0.0024 to 0.0067. Low and non-significant genetic differentiation was estimated among populations except for North Yellow Sea population, which has a significant genetic difference with other populations. The demographic history examined by mismatch distribution analyses and Bayesian skyline plot (BSP) analyses revealed that a sudden population expansion occurred almost 20 to 40 thousand years before. Relatively recent population expansion in the last glacial period, large dispersal of eggs or larvae carried by coastal current, and the homogeneity of living environment may have an important influence on the population genetic pattern.

Identification and occurrence of endogenous semicarbazide in prawns and crabs from Zhejiang Province, China.

Semicarbazide (SEM) is a side-chain metabolite of the antibiotic drug nitrofurazone (NFZ) and is employed as a conclusive marker for the use of banned NFZ. Recent studies have shown that SEM in aquatic crustaceans can be derived natively or from other sources. The presence and distribution of endogenous SEM within aquatic crustaceans is examined in this paper, which finds that the SEM content varies amongst the muscle, shell, and viscera of various prawn and crab species within the range of 0.35-26.62 ng g(-1). The effects of heating and hypochlorite treatment on SEM levels were examined. The results indicate that thermal processing introduced a more significant impact, resulting in a maximum SEM value of 15.48 ng g(-1) in a sample of shell of Portunus trituberculatus crab, while SEM levels in muscle samples were not affected by the duration of heating. Though 6% active chlorine treatment led to SEM production ranging between 39.9 and 196.4 ng g(-1) in muscle samples from various crustaceans, SEM is unlikely to originate from hypochlorite or chlorine in practice where there are limits to actual chlorine in sanitation water and facilities. 5-Nitro-2-furaldehyde (NF) was proposed as a selective marker to differentiate between endogenous SEM and NFZ-derived SEM in seafood.

Isolation and characterization of male-specific DNA markers in the rock bream Oplegnathus fasciatus.

Sex-specific DNA markers applicable were very useful for elucidating the sex-determination mechanism and sex control in fishes. In the present study, amplified fragment-length polymorphism (AFLP) approach with 144 primer combinations was employed to identify sex-specific markers in the rock bream. Four male-specific AFLP fragments were identified which were designated as Opl286, Opl237, Opl422, and Opl228. Further sequence analysis of the sex markers' genomic region revealed subtle differences between the males and females. We identified four male-specific single-nucleotide polymorphisms (SNPs) and a deletion of 8 bp in marker Opl286, six male-specific SNPs in marker Opl237, three male-specific SNPs in marker Opl422, and eight male-specific SNPs and 1 bp inversions in marker Opl228. Specific primers were designed based on the nucleotide variation in the sequences to develop a simple polymerase chain reaction method for identifying the genetic sex of rock bream. As a result, three out of the four male-specific markers were converted into SNP markers. The male-specific AFLP markers and AFLP-derived SNP markers were tested in 100 individuals collected from three locations around the coast of Zhoushan, yielding reproducible sex identification. These male-specific DNA markers are a useful tool for the identification of the sex-determining locus in rock bream and for guiding artificial breeding programs.

Simultaneous determination of albendazole and its metabolites in fish muscle tissue by stable isotope dilution ultra-performance liquid chromatography tandem mass spectrometry.

A rapid, specific, and sensitive method utilizing ultra-performance liquid chromatography tandem mass spectrometry was developed and validated to determine albendazole, albendazole sulfoxide, albendazole sulfone, and albendazole 2-aminosulfone in fish muscle tissue. The fish samples were extracted with ethyl acetate, then the organic phase was evaporated to dryness, and the residue was reconstituted in methanol-water solution and cleaned up by n-hexane. Reversed-phase separation of target compounds was achieved using a BEH C18 column and a gradient consisting of 0.2% (v/v) formic acid and methanol. Tandem mass spectrometry analyses were performed on a triple-quadrupole tandem mass spectrometer. In the whole procedure, the isotope-labeled internal standards were used to correct the matrix effect and variations associated with the analysis. The method was validated with respect to linearity, specificity, accuracy, and precision. The method exhibited a linear response from 0.1 to 20 ng mL(-1) (r(2) > 0.9985). The limit of quantitation for albendazole (ABZ), albendazole sulfoxide (ABZSO), albendazole sulfone (ABZSO(2)), and albendazole 2-aminosulfone (ABZ-2-NH(2)SO(2)) was 0.1, 0.1, 0.1, and 0.2 ng g(-1), respectively. The mean recoveries of ABZ, ABZSO, ABZSO(2), and ABZ-2-NH(2)SO(2) spiked at a level of 0.2-5.0 ng g(-1) were 95.3-113.7%, and the relative standard deviations of intra- and inter-day measurements were less than 6.38%. The method was later successfully applied to the determination of albendazole and its three metabolites in 60 fish samples collected from local markets.