Selective sweep analysis of the adaptability of the Yarkand hare (Lepus yarkandensis) to hot arid environments using SLAF-seq.

The Yarkand hare (Lepus yarkandensis) inhabits arid desert areas and is endemic to China. It has evolved various adaptations to survive in hot arid environments, including stress responses, the ability to maintain water homeostasis and heat tolerance. Here, we performed a selective sweep analysis to identify the candidate genes for adaptation to hot arid environments in the Yarkand hare. A total of 397 237 single-nucleotide polymorphisms were obtained from 80 Yarkand hares, which inhabit hot arid environments, and 36 Tolai hares (Lepus tolai), which inhabit environments with a mild climate, via specific-locus amplified fragment sequencing. We identified several candidate genes that were associated with the heat stress response (HSPE1), oxidative stress response (SLC23A and GLRX2), immune response (IL1R1 and IRG1), central nervous system development (FGF13, THOC2, FMR1 and MECP2) and regulation of water homeostasis (CDK1) according to fixation index values and θπ ratios in the selective sweep analysis, and six of these genes (GLRX2, IRG1, FGF13, FMR1, MECP2 and CDK1) are newly discovered genes. To the best of our knowledge, this is the first study to identify candidate genes for adaptation to hot arid environments in the Yarkand hare. The results of this study enhance our understanding of the adaptation of the Yarkand hare to hot arid environments and will aid future studies aiming to functionally verify these candidate genes.

Changes in the nutrients, phytochemical profile and antioxidant activity of Rheum officinale Baill. leaf blades during different growth periods.

Rhubarb contains an abundance of compounds and nutrients that promote health through various activities; however, these activities are affected by the harvest season. In this paper, the changes in nutrients, phytochemical profiles and antioxidant activity of Rheum officinale leaf blades (LRO) during different growth periods were investigated. The results showed that LRO is a good source of protein, fiber, and minerals and contains abundant fatty acids; however, as the harvest time increased from March to July, the levels of protein and amino acid decreased, and the levels of other nutrients reached a maximum in May or June. LRO also contains flavonoids, terpenoids, and quinones. As the harvest time increased, the quinone content decreased, possibly due to the unstable chemical properties of quinones at high temperatures. The flavonoid contents reached a maximum in May or June. This study indicated that LRO is a source of nutrients and chemical components and can be used for functional food production. In addition, the nutrients and chemical components related to the antioxidant activity of LRO changed according to the harvest season.

Dual roles of goethite coating on the transport of plastic nanoparticles in heterogeneous porous media: The significance of collector surface roughness.

This study systematically examines the roles of positive goethite on the retention and release of negative plastic nanoparticles (PSNPs) with different surface functional groups (Blank, -COOH, and -NH2). It provides the first evidence for the dual roles of goethite coatings on colloid transport; e.g., increased transport caused by surface morphology modification or decreased transport due to increased surface roughness and charge heterogeneity. Although previous work has shown that goethite-coated sand increases the retention of negative colloids, this work demonstrates that collector surface roughness can also reduce the retention of PSNPs due to increased interaction energy profiles. Nonmonotonic retention of all the different functionalized PSNPs was observed in goethite-coated rough sand, and the magnitude of variations was contingent on the PSNP functionalization, the solution ionic strength (IS), and the goethite coating. The release of PSNPs with IS decrease (phase I) and pH increase (phase II) varied significantly due to differences in energy barriers to detachment, e.g., release in phase I was inhibited in both goethite-coated sands, whereas release in phase II was enhanced in coated smooth sand but completely inhibited in rough sand. The findings of this study provide innovative insight into transport mechanisms for colloidal and colloid-associated contaminants.

Orally Administered Lactobacillus rhamnosus CY12 Alleviates DSS-Induced Colitis in Mice by Restoring the Intestinal Barrier and Inhibiting the TLR4-MyD88-NF-κB Pathway via Intestinal Microbiota Modulation.

Oral ingestion of probiotics is a promising approach to relieving inflammatory disease through regulating the gut microbiota. A newly discovered strain, Lactobacillus rhamnosus CY12 (LCY12), obtained from cattle-yak milk, displayed numerous probiotic properties. These included enhanced viability in low pH and bile environments, adhesion capabilities, and potent antimicrobial effects. The research aimed to explore the beneficial impacts of the novel LCY12 strain on colitis in mice induced by dextran sulfate sodium (DSS) and to elucidate the underlying molecular mechanisms. The results of the study showed that administration of LCY12 effectively helped to reduce the negative effects of DSS-induced body weight loss, disease activity index score, colon length shortening, loss of goblet cells, and overall histopathological scores in the intestines. Simultaneously, LCY12 administration significantly alleviated intestinal inflammation and safeguarded intestinal barrier integrity by enhancing IL-10 levels, while dampening IL-6, IL-1ß, and TNF-α production. Additionally, LCY12 boosted the presence of tight junction proteins. Furthermore, LCY12 hindered the TLR4/MyD88/NF-κB signaling pathway by downregulating TLR4 and MyD88 expression, inactivating phosphorylated IκBα, and preventing translocation of NF-κB p65 from the cytoplasm to the nucleus. The LCY12 also increased specific intestinal microbial communities and short-chain fatty acid (SCFA) production. Altogether, LCY12 oral administration alleviated colitis induced with DSS in mice by improving intestinal barrier function and regulating inflammatory cytokines, SCFA production, and intestinal microbiota.

Airborne signals of Pseudomonas fluorescens modulate swimming motility and biofilm formation of Listeria monocytogenes in a contactless coculture system.

Bacterial volatile compounds (BVCs) facilitate interspecies communication in socio-microbiology across physical barriers, thereby influencing interactions between diverse species. The impact of BVCs emitted from Pseudomonas on the biofilm formation characteristics of Listeria monocytogenes within the same ecological niche has been scarcely investigated under practical conditions of food processing. The objective of this study was to explore the motility and biofilm formation characteristics of L. monocytogenes under the impact of Pseudomonas BVCs. It was revealed that BVCs of P. fluorescens, P. lundensis, and P. fragi significantly promoted swimming motility of L. monocytogenes (P < 0.05). As evidenced by crystal violet staining, the L. monocytogenes biofilms reached a maximum OD570 value of approximately 3.78 at 4 d, which was 0.65 units markedly higher than that of the control group (P < 0.05). Despite a decrease in adherent cells of L. monocytogenes biofilms among the BVCs groups, there was a remarkable increase in the abundance of extracellular polysaccharides and proteins with 3.58 and 4.90 µg/cm2, respectively (P < 0.05), contributing to more compact matrix architectures, which suggested that the BVCs of P. fluorescens enhanced L. monocytogenes biofilm formation through promoting the secretion of extracellular polymers. Moreover, the prominent up-regulated expression of virulence genes further revealed the positive regulation of L. monocytogenes under the influence of BVCs. Additionally, the presence of BVCs significantly elevated the pH and TVB-N levels in both the swimming medium and biofilm broth, thereby exhibiting a strong positive correlation with increased motility and biofilm formation of L. monocytogenes. It highlighted the crucial signaling regulatory role of BVCs in bacterial interactions, while also emphasizing the potential food safety risk associated with the hitchhiking behavior of L. monocytogenes, thereby shedding light on advancements in control strategies for food processing.

Study of the transfer of Shiga toxin-producing Escherichia coli during the slaughter of cattle using molecular typing combined with epidemiologic data.

Investigation on the distribution and biological characteristics of Shiga-toxin producing Escherichia coli (STEC) during beef processing is essential for in-plant critical control points and food safety risk assessment. Serogroups and subtypes of stx genes of STEC strains isolated from beef processing lines were first investigated. Identification to cross-contamination among different sampling sites was further conducted by combining multilocus sequence typing (MLST) with the previous distribution and characterization data. The PCR-positive rate for STEC in 435 samples from two slaughter plants in China was 14.3% and the isolation rate for the 62 PCR positive and the entire set of 435 samples were 26% and 3.68% respectively. The existence of serotype O157:H7 (33%) and serogroups O121 (42%) and O26 (21%) as well as the high detection rate of high pathogenic gene stx2a (68%) in these serogroups indicated potential risk to the safety of beef. Traceability analysis showed that hide plays a critical role in cross-contamination between feces, lairage pens and post-washing carcasses from a molecular perspective. Intervening measures revolves around de-hiding should be involved in the in-plant safety control policy according to the tracing analysis.

Plateau pika fecal microbiota transplantation ameliorates inflammatory bowel disease manifestations in a mouse model of colitis.

Inflammatory bowel disease (IBD) is a serious global public health concern. Although the pathogenesis of the disease is currently unknown, it has been reported to be associated with both intestinal microbiota and inflammatory mediators. There is evidence suggesting that the feces of the Plateau pika is useful for treating gastrointestinal injuries and pain. Although fecal microbiota transplantation is highly efficacious intervention for IBD prevention, however, potential the transfer of pathogenic microbes or toxic substances is potentially hazardous. Fortunately, micropore filtering of the donor feces can minimize the risk of bacterial infection allowing retention of the therapeutic effects of the residual bacteriophages. Here, we demonstrated that Plateau pika feces not only alleviated the IBD symptoms but also promoted optimal structure and composition of the intestinal microbiota. Additionally, Plateau pika feces transfer also enhanced phenotypic features, such as, body-weight, disease activity index, and histological scores. In conclusion, Plateau pika feces was found to protect mice against colitis induced by dextran sodium sulfate by reducing inflammation and regulating microbial dysbiosis. These findings suggest the potential of Plateau pika feces as an alternative therapy for IBD.

Retention and release of black phosphorus nanoparticles in porous media under various physicochemical conditions.

Black phosphorus nanosheets/nanoparticles (BPNs) are widely applied in many fields. However, the transport of BPNs in the subsurface still has not yet been reported and there is increasing concern about potential adverse impacts on ecosystems. Roles of median grain size and surface roughness, BPN concentration, and solution chemistries (pH, ionic strength, and cation types) on the retention and release of BPNs in column experiments were therefore investigated. The mobility of BPNs significantly increased with increasing grain size and decreasing surface roughness due to their influence on the mass transfer rate, number of deposition sites and retention capacity, and straining processes. Transport of BPNs was enhanced with an increase in pH and a decrease in ionic strength because of surface deprotonation and stronger repulsion that tends to reduce aggregation. The BPN transport was significantly sensitive to ionic strength, compared with other engineered nanoparticles. Additionally, charge heterogeneity and cation-bridging played a critical role in the retention of BPNs in the presence of divalent cations. Higher input concentrations increased the retention of BPNs, probably because collisions, aggregation at pore throat locations, and hydrodynamic bridging were more pronounced. Small fractions of BPNs can be released under decreasing IS and increasing pH due to the expansion of the electrical double layer and increased repulsion at convex roughness locations. A mathematical model that includes provisions for advective dispersive transport and time-dependent retention with blocking or ripening terms well described the retention and release of BPNs. These findings provide fundamental information that helps to understand the transport of BPNs in the subsurface environments.

Corrigendum: Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers.

[This corrects the article DOI: 10.3389/fgene.2022.1018632.].

Preliminary investigation into the prediction of indicators of beef spoilage using Raman and Fourier transform infrared spectroscopy.

The objective of this study was to assess the potential to predict the microbial beef spoilage indicators by Raman and Fourier transform infrared (FT-IR) spectroscopies. Vacuum skin packaged (VSP) beef steaks were stored at 0 °C, 4 °C, 8 °C and under a dynamic temperature condition (0 °C âˆ¼ 4 °C âˆ¼ 8 °C, for 36 d). Total viable count (TVC) and total volatile basic nitrogen (TVB-N) were obtained during the storage period along with spectroscopic data. The Raman and FTIR spectra were baseline corrected, pre-processed using Savitzky-Golay smoothing and normalized. Subsequently partial least squares regression (PLSR) models of TVC and TVB-N were developed and evaluated. The root mean squared error (RMSE) ranged from 0.81 to1.59 (log CFU/g or mg/100 g) and the determination coefficient (R2) from 0.54 to 0.75. The performance of PLSR model based on data fusion (combination of Raman and FT-IR data) is better than that based on Raman spectra and similar to that of FT-IR. Overall, Raman spectroscopy, FT-IR spectroscopy, and a combination of both exhibited a potential for the prediction of the beef spoilage.

The role of PhoP/PhoQ system in regulating stress adaptation response in Escherichia coli O157:H7.

The development of acid tolerance response (ATR) as a result of low pH in Escherichia coli O157:H7 (E. coli O157:H7) contaminating beef during processing is considered a major food safety concern. Thus, in order to explore the formation and molecular mechanisms of the tolerance response of E. coli O157:H7 in a simulated beef processing environment, the resistance of a wild-type (WT) strain and its corresponding ΔphoP mutant to acid, heat, and osmotic pressure was evaluated. Strains were pre-adapted under different conditions of pH (5.4 and 7.0), temperature (37 °C and 10 °C), and culture medium (meat extract and Luria-Bertani broth media). In addition, the expression of genes related to stress response and virulence was also investigated among WT and ΔphoP strains under the tested conditions. Pre-acid adaptation increased the resistance of E. coli O157:H7 to acid and heat treatment while resistance to osmotic pressure decreased. Moreover, acid adaptation in meat extract medium simulating slaughter environment increased ATR, whereas pre-adaptation at 10 °C reduced the ATR. Furthermore, it was shown that mildly acidic conditions (pH = 5.4) and the PhoP/PhoQ two-component system (TCS) acted synergistically to enhance acid and heat tolerance in E. coli O157:H7. Additionally, the expression of genes related to arginine and lysine metabolism, heat shock, and invasiveness was up-regulated, which revealed that the mechanism of acid resistance and cross-protection under mildly acidic conditions was mediated by the PhoP/PhoQ TCS. Both acid adaptation and phoP gene knockout reduced the relative expression of stx1 and stx2 genes which were considered as critical pathogenic factors. Collectively, the current findings indicated that ATR could occur in E. coli O157:H7 during beef processing. Thus, there is an increased food safety risk due to the persistence of tolerance response in the following processing conditions. The present study provides a more comprehensive basis for the effective application of hurdle technology in beef processing.

Potential inhibitory effect of carbon dioxide on the spoilage behaviors of Pseudomonas fragi in high-oxygen packaged beef during refrigerated storage.

Pseudomonas fragi is a dominant meat spoilage organism under high-oxygen modified atmosphere packaging (HiOx-MAP). This work investigated the effects of CO2 on P. fragi growth and the related spoilage phenomena of HiOx-MAP beef. Minced beef incubated with P. fragi T1, a strain owning the strongest spoilage potential among isolates, was stored under CO2-enriched HiOx-MAP (TMAP; 50% O2/40% CO2/10% N2) or non-CO2 HiOx-MAP (CMAP; 50% O2/50% N2) at 4 °C for 14 days. Compared to CMAP, TMAP maintained sufficient O2 levels to endow beef with higher a* values and meat color stability due to lower P. fragi counts from day 1 (P < 0.05). TMAP samples also showed lower (P < 0.05) lipase activity and protease activity within 14-days and 6-days than CMAP samples respectively. TMAP delayed the significantly increased pH and total volatile basic nitrogen contents occurred in CMAP beef during storage. Despite TMAP markedly promoted the lipid oxidation associated with higher concentrations of hexanal and 2,3-octanedione than CMAP (P < 0.05), TMAP beef retained an acceptable organoleptic odor due to a CO2-inhibition on the microbial-induced 2,3-butanedione and ethyl 2-butenoate formation. This study provided a comprehensive insight into the antibacterial mechanism of CO2 on P. fragi in HiOx-MAP beef.

The Prevalence and Antibiotic-Resistant of Listeria monocytogenes in Livestock and Poultry Meat in China and the EU from 2001 to 2022: A Systematic Review and Meta-Analysis.

To compare the prevalence and antibiotic resistance rate of Listeria monocytogenes in livestock and poultry (beef, pork and chicken) meat between China and the European Union (EU), a meta-analysis was conducted. Ninety-one out of 2156 articles in Chinese and English published between January 2001 and February 2022 were selected from four databases. The prevalence of L. monocytogenes in livestock and poultry (beef, pork and chicken) meat in China and Europe was 7.1% (3152/56,511, 95% CI: 5.8-8.6%) and 8.3% (2264/889,309, 95% CI: 5.9-11.0%), respectively. Moreover, a decreasing trend was observed in both regions over time. Regarding antibiotic resistance, for the resistance to 15 antibiotics, the pooled prevalence was 5.8% (95% CI: 3.1-9.1%). In both regions, the highest prevalence was found in oxacillin, ceftriaxone and tetracycline, and a large difference was reported between China and the EU in ceftriaxone (52.6% vs. 17.3%) and cefotaxime (7.0% vs. 0.0%). Based on the above, it remains a significant challenge to enforce good control measures against the meat-sourced L. monocytogenes both in China and in the EU.

The biological effect of a beef-derived Latilactobacillus sakei on beef steaks during chilled storage.

The aim of this study was to investigate the biological inhibiting effect of a beef-derived Latilactobacillus sakei (RS-25) on the spoilage of beef steaks in overwrapped packaging during the 12 days of storage at 4°C. Beef quality as well as microbial indicators were determined at different intervals during the storage after the inoculation of RS-25 at the 6 log CFU/g, and the high-throughput sequencing was applied to investigate the changes of microbial community structure during the storage. The inoculation of RS-25 on beef had no effect (p > .05) on pH, TBARS, and TVB-N during storage indicating the weak effect of such strain on the eat quality. Furthermore, the rise of L* and the delayed decline of a* and b* reveal the protection effect of RS-25 on the meat color. RS-25 reduced the re-contaminated Salmonella typhimurium by 1.16 log CFU/g (p < .01), and the growth of Brochothrix thermosphacta was also inhibited but no inhibition was found on the Pseudomonas spp. at the first 6 days of storage. The inhibiting effect of RS-25 was covered by the rapid growth of other microorganism during the following 6 days of storage. Consistent with the microbial counts results, high-throughput sequencing analysis confirmed that the inoculated L. sakei RS-25 was dominant at first 6 days, and then replaced by Pseudomonas spp. The findings obtained from the current study may provide basic information for the further application of bioprotective bacteria in preservation of beef steaks in the overwrapped packaging.

Influence of low-energy electron beam irradiation on the quality and shelf-life of vacuum-packaged pork stored under chilled and superchilled conditions.

This study aimed to explore the effects of different levels (0, 8, and 12 kGy) of low-energy electron beam (LEEB; 0.2 MeV) on the quality and shelf-life of vacuum-packaged pork stored under chilled and superchilled conditions for 30 days. LEEB irradiation promoted lipid and protein oxidation, regardless of the levels used. Combined 8 kGy LEEB irradiation with superchilled storage significantly elevated a* values and preserved acceptable sensory characteristics of pork until day 30, unlike the other treatment combinations. This synergistic treatment also significantly reduced total viable counts and total volatile basic nitrogen contents, and thus extended the shelf-life of vacuum-packaged pork to >30 days, which may be due to the antibacterial effects on Photobacterium, Carnobacterium and Lactobacillus. In conclusion, it is recommended that the 8 kGy LEEB irradiation level be applied to pork and that it should be used in combination with superchilled storage to preserve meat quality and extend the shelf-life of vacuum-packaged pork.

Sensitivity of the Transport of Plastic Nanoparticles to Typical Phosphates Associated with Ionic Strength and Solution pH.

The influence of phosphates on the transport of plastic particles in porous media is environmentally relevant due to their ubiquitous coexistence in the subsurface environment. This study investigated the transport of plastic nanoparticles (PNPs) via column experiments, paired with Derjaguin-Landau-Verwey-Overbeek calculations and numerical simulations. The trends of PNP transport vary with increasing concentrations of NaH2PO4 and Na2HPO4 due to the coupled effects of increased electrostatic repulsion, the competition for retention sites, and the compression of the double layer. Higher pH tends to increase PNP transport due to the enhanced deprotonation of surfaces. The release of retained PNPs under reduced IS and increased pH is limited because most of the PNPs were irreversibly captured in deep primary minima. The presence of physicochemical heterogeneities on solid surfaces can reduce PNP transport and increase the sensitivity of the transport to IS. Furthermore, variations in the hydrogen bonding when the two phosphates act as proton donors will result in different influences on PNP transport at the same IS. This study highlights the sensitivity of PNP transport to phosphates associated with the solution chemistries (e.g., IS and pH) and is helpful for better understanding the fate of PNPs and other colloidal contaminants in the subsurface environment.

The underlying mechanisms of the effect of superchilling on the tenderness of beef Longissimus lumborum.

This study investigated the effect of superchilling (-30 °C until the core temperature achieved -3 °C, then stored at -1 °C until 24 h, SC) on the tenderness of hot boned beef M. longissimus lumborum (LL), with very fast chilling (-30 °C until the core temperature achieved 0 °C, then stored at -1 °C until 24 h, VFC) and conventional chilling (0- 4 °C for 24 h, CC) as the controls. The lowest initial shear force values were obtained in SC samples compared to those from the VFC and CC treatments (P < 0.05). Clear freezing damage of muscle fibers and more myofibril fragmentation were found in SC samples compared with the other samples early post-mortem. Moreover, SC samples showed the highest level of inosine 5-monophosphate at 3 h post-mortem (P < 0.05). A reduced glycolysis rate (as evidenced by lactate content) was also found in SC treated samples suggesting little contribution of glycolysis on the tenderization of SC.

Processing interventions for enhanced microbiological safety of beef carcasses and beef products: A review.

Chilled beef is inevitably contaminated with microorganisms, starting from the very beginning of the slaughter line. A lot of studies have aimed to improve meat safety and extend the shelf life of chilled beef, of which some have focused on improving the decontamination effects using traditional decontamination interventions, and others have investigated newer technologies and methods, that offer greater energy efficiency, lower environmental impacts, and better assurances for the decontamination of beef carcasses and cuts. To inform industry, there is an urgent need to review these interventions, analyze the merits and demerits of each technology, and provide insight into 'best practice' to preserve microbial safety and beef quality. In this review, the strategies and procedures used to inhibit the growth of microorganisms on beef, from slaughter to storage, have been critiqued. Critical aspects, where there is a lack of data, have been highlighted to help guide future research. It is also acknowledge that different intervention programs for microbiological safety have different applications, dependent on the initial microbial load, the type of infrastructures, and different stages of beef processing.

Effects of low-energy electron beam irradiation on the shelf-life and quality of vacuum-packaged beef steaks during chilled storage.

This study evaluated the effects of different doses (0, 4, 8, 12, 16 kGy) of low-energy electron beam (LEEB; 0.2 MeV) on the quality changes of vacuum-packaged beef steaks during chilled storage for 21 days. LEEB irradiation at a low dose (4 and 8 kGy) significantly elevated the L* values of steaks, and did not deteriorate the a* values, the oxidation of lipid and protein (P > 0.05) compared to non-irradiated samples. LEEB irradiation (4 and 8 kGy) also significantly reduced the bacterial loads compared with non-irradiated steak, which may be due to the inactivation effect on Acinetobacter, Brochothrix thermosphacta, Carnobacterium divergens, Leuconostoc and Serratia during storage. Albeit all doses retained more acceptable sensory characteristics compared to non-irradiated samples, LEEB irradiation with >8 kGy significantly reduced the L* values and promoted protein oxidation. Overall, the LEEB irradiation with 4-8 kGy could be used as a promising innovative technology for extending the shelf-life of vacuum-packaged chilled beef steaks.

Effect of the combination of superchilling and super-chilled storage on shelf-life and bacterial community dynamics of beef during long-term storage.

This study investigated the effect of superchilling (-30 °C until the core temperature achieved -3 °C, and - 1 °C until 24 h, SC) on shelf-life and bacterial community dynamics of beef loins, with a typical very fast chilling (-30 °C until the core temperature achieved 0 °C, and - 1 °C until 24 h, VFC) and conventional chilling (0- 4 °C for 24 h, CC) as controls. The super-chilled storage (-1 °C) was adopted after each chilling procedure, and physicochemical traits and microbiological quality were evaluated during a long-term storage. No remarkable adverse impact on meat color and lipid oxidation were observed in SC treatment. The bacterial composition results showed that Carnobacterium spp. were the main bacteria in SC treatment in the late storage period (63- 84 days). The loss of Lactobacillus spp., due to the "ultra-low temperature" during the superchilling, might be the reason that the SC did not result in a longer shelf-life compared with CC samples.