Physiological Adaptation of Fenneropenaeus chinensis in Response to Saline-Alkaline Stress Revealed by a Combined Proteomics and Metabolomics Method.

The rapid development of the mariculture industry has been hindered by limited coastal aquaculture space. To utilize the abundant inland saline-alkaline water, we studied the physiological effects of high carbonate alkalinity stress and high pH stress on Fenneropenaeus chinensis. The study employed quantitative proteomics by tandem mass tag (TMT) and non-targeted metabolomics analysis using a liquid chromatograph mass spectrometer (LC-MS) to understand the physiological and biochemical adaptive mechanisms of the hepatopancreas of F. chinensis in response to saline-alkaline stress at the molecular level. We designed two stress groups as follows: a high carbonate alkalinity (CA) group and a combined high carbonate alkalinity and high pH (CP) group. The study found that the protein and metabolic profiles of the two stress groups were changed, and the CP group, which was exposed to dual stresses, incurred more severe damage to the hepatopancreas compared to that of the CA group. After exposure to CA and CP, the hepatopancreas of F. chinensis showed significant alterations in 455 proteins and 50 metabolites, and 1988 proteins and 272 metabolites, respectively. In addition, F. chinensis upregulated the level of energy metabolism in the hepatopancreas to defend against osmotic imbalance caused by CA or CP stress, which was demonstrated by the significant upregulation of important proteins and metabolites in glycolysis, pyruvate metabolism, TCA cycle, and fatty acid oxidation. Additionally, pattern recognition receptors, the phenol oxidase system, and various immune-related metabolic enzymes and metabolites were also affected. The immune homeostasis of F. chinensis was affected by the alteration of the antioxidant system following exposure to CA or CP. These findings provide valuable information for F. chinensis saline-alkaline water cultivation practices.

Solid-liquid partitioning and speciation of Pb(II) and Cd(II) on goethite under high pH conditions, as examined by subnanomolar heavy metal analysis, X-ray absorption spectroscopy, and surface complexation modeling.

The adsorption of heavy metals on iron oxides generally increases with pH and is almost complete at neutral to slightly alkaline pH. However, almost complete adsorption on a linear scale does not imply sufficient removal of the heavy metals in terms of their toxicity. Here, we elucidated the chemical reactions that determine the solid-liquid partitioning of Pb(II) and Cd(II) on goethite at high pH. While the removal of both heavy metals was almost complete on a linear scale above pH 7 for Pb(II) and pH 9 for Cd(II), the dissolved metal concentrations decreased on a logarithmic scale with pH, reaching minima at around pH 10 for Pb(II) and pH 10-11 for Cd(II), and then they increased with pH thereafter. The XAFS spectra of Pb(II)- or Cd(II)-adsorbed goethite prepared at pH > 11 were almost the same as those at neutral pH, suggesting that removal of the heavy metals from solution was achieved by a single adsorption reaction over the entire pH range. Based on the observed macroscopic and microscopic adsorption behaviors at high pH, a robust surface complexation model was developed to predict the solid-liquid partitioning of divalent heavy metals over the entire pH range.

Iron coupled with hydroxylamine turns on the "switch" for free radical degradation of organic pollutants under high pH conditions.

Reducing iron by hydroxylamine (HA) can promote the generation of reactive oxygen species (ROS) in the Fenton reaction and play a crucial role in the degradation of organic pollutants. However, the performance of this system at wider environmental thresholds is still not sufficiently understood, especially in the highly alkaline environments resulting from human activities. Here, we assessed the impact of solution pH on organic pollutant degradation by goethite with the addition of HA and H2O2. The solid phase variation and ROS generation were analyzed using Mössbauer spectroscopy, X-ray absorption near edge structure spectroscopy, and electron paramagnetic resonance analysis. This study found that under alkaline conditions, the system can continuously scavenge organic pollutants through oxygen-mediated generation of free radicals. At lower pH levels, organic pollutant decomposition, exemplified by the breakdown of bisphenol A (BPA), is primarily driven by the Fenton reaction facilitated by iron. As pH increases, hydroxyl radical (•OH) production decreases, accompanied by decreased BPA removal efficiency. However, the removal efficiency of BPA increased significantly at pH > 9. At pH 12, the removal of BPA exceeded that of the acidic condition after one hour, which is consistent with observations in soil system studies. Unlike the Fenton reaction, which is not sensitive to oxygen content, the removal of BPA under alkaline conditions occurs only under aerobic conditions. H2O2 is hardly involved in the reaction, and the depletion of HA becomes a critical factor in the decomposition of BPA. Importantly, in contrast to acidic conditions, where the dramatic decomposition of BPA occurs mainly in the first 10 min, the decomposition of BPA under alkaline conditions continued to occur over the 2 h of observation until complete removal. For natural systems, the remediation of pollutants depends more on the active time of ROS than on their reactivity. Therefore, this idea can reference pollution remediation strategies in anthropogenically disturbed environments.

The coupling of sulfide and Fe-Mn mineral promotes the migration of lead and zinc in the redox cycle of high pH floodplain soils.

In this study, we investigated the impact of fluctuating water levels on the distribution of lead (Pb) and zinc (Zn) in soil and sediments at a historical Pb-Zn smelting site along the Xiangjiang River. Despite the high pH levels (7 to 11) in the study area, which generally inhibits heavy metal solubility, we found that regular changes in water levels still affect Pb-Zn movement. Soil analysis revealed distinct redox zones within the unconfined aquifer, as shown by the variable Fe/Mn and Ce/Ce* ratios. Advanced techniques such as Mn K-edge XAFS, Mössbauer spectroscopy, and TOF-SIMS indicated persistent Fe-Mn redox cycling and highlighted the presence of Pb and Zn-rich manganese oxides near sulfur-bearing minerals. These findings suggest that acidic microzones produced by the oxidation of sulfur-bearing minerals become "refuges" for microbial and heavy metal activity. Considering that sulfur-containing minerals are widespread waste types in nonferrous metal smelting sites, these findings are instructive for a better understanding of the transformation mechanisms of heavy metal ions in nonferrous metal smelting-polluted environments and for guiding pollution remediation strategies.

Genome-wide characterization, transcriptome profiling, and functional analysis of the ALMT gene family in Medicago for aluminum resistance.

Aluminum (Al) is the major limiting factor affecting plant productivity in acidic soils. Al3+ ions exhibit increased solubility at a pH below 5, leading to plant root tip toxicity. Alternatively, plants can perceive very low concentrations of Al3+, and Al triggers downstream signaling even at pH 5.7 without causing Al toxicity. The ALUMINUM-ACTIVATED-MALATE-TRANSPORTER (ALMT) family members act as anion channels, with some regulating the secretion of malate from root apices to chelate Al, which is a crucial mechanism for plant Al resistance. To date, the role of the ALMT gene family within the legume Medicago species has not been fully characterized. In this study, we investigated the ALMT gene family in M. sativa and M. truncatula and identified 68 MsALMTs and 18 MtALMTs, respectively. Phylogenetic analysis classified these genes into five clades, and synteny analysis uncovered genuine paralogs and orthologs. The real-time quantitative reverse transcription PCR (qRT-PCR) analysis revealed that MtALMT8, MtALMT9, and MtALMT15 in clade 2-2b are expressed in both roots and root nodules, and MtALMT8 and MtALMT9 are significantly upregulated by Al in root tips. We also observed that MtALMT8 and MtALMT9 can partially restore the Al sensitivity of Atalmt1 in Arabidopsis. Moreover, transcriptome analysis examined the expression patterns of these genes in M. sativa in response to Al at both pH 5.7 and pH 4.6, as well as to protons, and found that Al and protons can independently induce some Al-resistance genes. Overall, our findings indicate that MtALMT8 and MtALMT9 may play a role in Al resistance, and highlight the resemblance between the ALMT genes in Medicago species and those in Arabidopsis.

pH inactivation of SARS-CoV-2 and SARS-CoV in virus spiked protein A eluates from a mAb purification process.

Biopharmaceutical manufacturing processes may include a low pH treatment step as a means of inactivating enveloped viruses. Small scale virus clearance studies are routinely performed using model enveloped viruses such as murine leukemia virus to assess inactivation at the pH range used in the downstream manufacturing process. Further, as a means of bioburden reduction, chromatography resins may be cleaned and stored using sodium hydroxide and this can also inactivate viruses. The susceptibility of SARS-CoV-2 and SARS-CoV to low pH conditions using protein A eluate derived material from a monoclonal antibody production process as well as high pH cleaning conditions was addressed. SARS-CoV-2 was effectively inactivated at pH 3.0, moderately inactivated at pH 3.4, but not inactivated at pH 3.8. Low pH was less effective at inactivating SARS-CoV. Both viruses were inactivated at a high pH of ca.13.4. These studies provide important information regarding the effectiveness of viral clearance and inactivation steps of novel coronaviruses when compared to other enveloped viruses.

Rapid purification of mAb using protein a membranes yielding high HCP clearance.

Protein A chromatography remains the crucial step in mAb purification because of the high binding specificity and impurity clearance. In recent years, highly productive membrane adsorbers emerged as an alternative to traditional resins allowing for rapid purification of biomolecules. In this study, we tested three commercially available protein A membranes (Sartobind® Rapid A, HiTrap Fibro™ PrismA and GORE™ Protein Capture Device) regarding flow distribution, permeability and binding performance. As an application study using a cell-culture supernatant (CCS) containing monoclonal antibodies (mAbs), acidic and high pH wash steps were investigated regarding recovery and impurity removal. All membranes proved their applicability as highly productive capture media leading to high HCP and DNA removal with no observable influence on recovery. GORE™ Protein Capture Device exhibited a superior flow distribution but revealed diffusional limitations at high flow rates. Sartobind® Rapid A and HiTrap Fibro™ PrismA showed binding capacities of âˆ¼ 40 g/L even at residence times (RTs) < 12 s but were limited by hydrodynamics suggesting room for improvement with optimized membrane housing.

Hydrophobic Derivatization Strategy Facilitates Comprehensive Profiling of Protein Methylation.

Protein methylation is receiving more and more attention due to its essential role in diverse biological processes. Large-scale analysis of protein methylation requires the efficient identification of methylated peptides at the proteome level; unfortunately, a significant number of methylated peptides are highly hydrophilic and hardly retained during reversed-phase chromatography, making it difficult to be identified by conventional approaches. Herein, we report the development of a novel strategy by combining hydrophobic derivatization and high pH strong cation exchange enrichment, which significantly expands the identification coverage of the methylproteome. Noteworthily, the total number of identified methylated short peptides was improved by more than 2-fold. By this strategy, we identified 492 methylation sites from NCI-H460 cells compared to only 356 sites identified in native forms. The identification of methylation sites before and after derivatization was highly complementary. Approximately 2-fold the methylation sites were obtained by combining the results identified in both approaches (native and derivatized) as compared with the only analysis in native forms. Therefore, this novel chemical derivatization strategy is a promising approach for the comprehensive identification of protein methylation by improving the identification of methylated short peptides.

Bicarbonate rather than high pH in growth medium induced Fe-deficiency chlorosis in dwarfing rootstock quince A (Cydonia oblonga Mill.) but did not impair Fe nutrition of vigorous rootstock Pyrus betulifolia.

Introduction: Quince A (Cydonia oblonga Mill.), a typical dwarfing rootstock in pear cultivation, is susceptible to iron (Fe) deficiency in calcareous soils. The aim of this study was to compare the strategies in Fe uptake and utilization in dwarfing rootstock quince A (low Fe efficiency) versus a typical vigorous rootstock Pyrus betulifolia (PB) with high Fe efficiency. Methods: Quince A and PB were grown in nutrient solution (pH 6.3) for 4 weeks followed by three pH treatments: pH6.3, pH8.3a (adjusted with hydroxide) and pH8.3b (adjusted with bicarbonate). The Fe uptake and utilization indicators of the rootstocks were assessed at the onset of chlorosis symptoms (after 58 days of treatments). Results and discussion: In contrast to PB, quince A exhibited Fe deficiency chlorosis under bicarbonate (pH8.3b). Bicarbonate stimulated the root proton secretion, inhibited root growth and ferric chelate reductase (FCR) activity in both PB and quince A, whereas high pH without bicarbonate (pH8.3a) stimulated only root proton release. Both species accumulated more Fe in roots under high pH treatments than under pH6.3, resulting in Fe sufficiency in leaves. Both high pH treatments increased the activity of leaf FCR in PB and quince A. However, extractable Fe(II) concentration in leaves was increased by high pH treatments in PB only. This study demonstrated that depressed Fe(III) reduction in leaves caused by bicarbonate rather than high pH explained Fe deficiency in quince A grown in bicarbonate-containing medium.

A micro-flow, high-pH, reversed-phase peptide fractionation and collection system for targeted and in-depth proteomics of low-abundance proteins in limiting samples.

We present a method and a simple system for high-pH RP-LC peptide fractionation of small sample amounts (30-60 µg), at micro-flow rates with micro-liter fraction collection using ammonium bicarbonate as an optimized buffer for system stability and robustness. The method is applicable to targeted mass spectrometry approaches and to in-depth proteomic studies where the amount of sample is limited. Using targeted proteomics with peptide standards, we present the method's analytical parameters, and potential in increasing the detection of low-abundance proteins that are difficult to quantify with direct targeted or global LC-MS analyses. This fractionation system increased peptide signals by up to 18-fold, while maintaining high quantitative precision, with high fractionation reproducibility across varied sample sets. In real applications, it increased the detection of targeted endogenous peptides by two-fold in a 25 cell-cycle-control protein panel, and in-depth MS analyses of nuclear extracts, it allowed the detection of up to 8,896 proteins with 138,417 peptides in 24-concatenated fractions compared to 3,344 proteins with 23,093 peptides without fractionation. In a relevant biological problem of CDK4/6-inhibitors and breast cancer, the method reproduced known information and revealed novel insights, highlighting that it can be successfully applied in studies involving low-abundance proteins and limited samples. •Tested nine high-pH buffer/solvent systems to obtain a robust, effective, and reproducible micro-flow fractionation method which was devoid of commonly encountered LC clogging/pressure issues after months of use.•Peptide enrichment method to improve detection and quantitation of low-abundance proteins in targeted and in-depth proteomic studies.•Can be applied to diverse protein samples where the available amount is limited.

Microbial taxa related to natural hydrogen and methane emissions in serpentinite-hosted hyperalkaline springs of New Caledonia.

The southeastern part of New Caledonia main island (Grande Terre) is the location of a large ophiolitic formation that hosts several hyperalkaline springs discharging high pH (∼11) and warm (<40°C) fluids enriched in methane (CH4) and hydrogen (H2). These waters are produced by the serpentinization of the ultrabasic rock formations. Molecular surveys had previously revealed the prokaryotic diversity of some of these New Caledonian springs, especially from the submarine chimneys of Prony Bay hydrothermal field. Here we investigate the microbial community of hyperalkaline waters from on-land springs and their relationships with elevated concentrations of dissolved H2 (21.1-721.3 µmol/L) and CH4 (153.0-376.6 µmol/L). 16S rRNA gene analyses (metabarcoding and qPCR) provided evidence of abundant and diverse prokaryotic communities inhabiting hyperalkaline fluids at all the collected springs. The abundance of prokaryotes was positively correlated to the H2/CH4 ratio. Prokaryotes consisted mainly of bacteria that use H2 as an energy source, such as microaerophilic Hydrogenophaga/Serpentinimonas (detected in all sources on land) or anaerobic sulfate-reducing Desulfonatronum, which were exclusively found in the most reducing (Eh ref H2 ∼ -700 mV) and the most H2-enriched waters discharging at the intertidal spring of the Bain des Japonais. The relative abundance of a specific group of uncultured Methanosarcinales that thrive in serpentinization-driven ecosystems emitting H2, considered potential H2-consuming methanogens, was positively correlated with CH4 concentrations, and negatively correlated to the relative abundance of methylotrophic Gammaproteobacteria. Firmicutes were also numerous in hyperalkaline waters, and their relative abundance (e.g., Gracilibacter or Dethiobacter) was proportional to the dissolved H2 concentrations, but their role in the H2 budget remains to be assessed. The prokaryotic communities thriving in New Caledonia hyperalkaline waters are similar to those found in other serpentinite-hosted high-pH waters worldwide, such as Lost City (North Atlantic) and The Cedars (California).

Response of Diverse Peanut Cultivars to Nano and Conventional Calcium Forms under Alkaline Sandy Soil.

Calcium is one of the most limiting factors for the growth and reproduction of peanut, which ultimately affects pod and seed yields. A two-year field experiment was carried out to assess the impact of five calcium applications, including nano-calcium and conventional forms, on growth, leaf nutrient content, yield traits, and quality parameters of three diverse peanut cultivars (Ismailia-1, Giza-5, and Giza-6). The applied calcium applications were calcium sulfate, which is recommended for commercial peanut cultivation and commonly referred to as gypsum (coded as Ca-1), calcium nitrate (Ca-2), nano-calcium nitrate (Ca-3), 50% calcium nitrate + 50% nano-calcium (Ca-4), and 50% calcium sulfate + 50% nano-calcium (Ca-5). Calcium sulfate (gypsum, Ca-1) was soil-supplied during the seedbed preparation as recommended, while the other calcium applications (Ca-2, Ca-3, Ca-4, and Ca-5) were exogenously sprayed three times at 30, 45, and 60 days after sowing. The soil of the experimental site was alkaline, with a high pH of 8.6. The results revealed significant differences among cultivars, calcium applications, and their interactions. The soil-supplied gypsum Ca-1 displayed lower agronomic performance on all recorded growth, leaf nutrient content, yield traits, and quality parameters. On the other hand, the foliar-supplied calcium, particularly Ca-4 and Ca-5, displayed superior effects compared to the other simple calcium forms. Ca-4 and Ca-5 produced significantly higher seed yield (3.58 and 3.38 t/ha) than the simple recommended form (Ca-1, 2.34 t/ha). This could be due to the difficulty of calcium uptake from soil-supplied calcium under high soil pH compared to the exogenously sprayed nano-calcium form. Moreover, the superior performance of Ca-4 and Ca-5 could be caused by the mixture of fertilizers from the synergistic effect of calcium and nitrate or sulfate. Furthermore, the effect of nitrate was applied in nano form in the Ca4 and Ca-5 treatments, which contributed to improving nutrient uptake efficiency and plant growth compared to the other treatments. The peanut cultivar Giza-6 showed superiority for most measured traits over the other two cultivars. The interaction effect between the assessed cultivars and calcium applications was significant for various traits. The cultivar Giza-6 showed a significant advantage for most measured traits with the mixture of 50% calcium nitrate + 50% nano-calcium (Ca-4). Conclusively, the results pointed out the advantage of the exogenously sprayed nano-calcium form combined with calcium nitrate or calcium sulfate for promoting growth, leaf nutrient content, yield, and quality traits of peanut, particularly with high-yielding cultivars under sandy soil with high pH.

Analysis of growth resistance mechanisms and causes in tea plants (Camellia sinensis) in high-pH regions of Northern China.

Background: In tea plantations with high-pH (pH > 6.5) in Northern China, tea plants are prone to yellowing disease, albinism, and reductions in components that contribute to plant quality, which affect the scale and rate of tea plantation development in Northern China. Methods: To investigate the potential causes of these issues, Camellia sinensis cv. Pingyang Tezao and Camellia sinensis cv. Ruixue were planted in Shouguang city (a high-pH area, soil pH > 6.5) and Rizhao city (a normal-pH area, soil pH is 4.5-5.5), respectively; differences in growth morphology, pigment content, cell structure, quality-determining components, and element content of the two varieties in the two areas were analyzed. Results: The results showed that tea leaves planted in Shouguang had varying degrees of yellowing disease and albinism; the pigment content in both varieties was significantly lower when planted in Shouguang compared with Rizhao. The cell structure was severely damaged and the main quality-determining components were decreased. Nitrogen (N), phosphorus (P), potassium (K), zinc (Zn), copper (Cu) and manganese (Mn) contents in the leaves of the two tea plant varieties were significantly lower when planted in Shouguang compared with those in Rizhao; the levels of these elements in Shouguang soil were significantly higher than in Rizhao soil. Calcium (Ca) contents in Shouguang soil was 9.90 times higher than that of Rizhao soil. Conclusions: We conclude that the soil in high-pH areas hindered tea plant uptake of N, Zn, Cu, and Mn, which had a detrimental effect on chloroplasts and reductions in chlorophyll synthesis, contributing to yellowing disease and albinism. In addition, excessive calcium (Ca) in Shouguang soil was also an important contributor to these negative effects. High-pH soil hindered tea plant uptake of P and K, resulting in reductions in tea polyphenols, amino acids, and other major quality components.

Offline Peptide Fractionation and Parallel Reaction Monitoring MS for the Quantitation of Low-Abundance Plasma Proteins.

Mass spectrometry (MS)-based protein quantitation is an attractive means for research and diagnostics due to its high specificity, precision, sensitivity, versatility, and the ability to develop multiplexed assays for the "absolute" quantitation of virtually any protein target. However, due to the large dynamic range of protein concentrations in blood, high abundance proteins in blood plasma hinder the detectability and quantification of lower-abundance proteins which are often relevant in the context of different diseases. Here we outline a streamlined method involving offline high-pH reversed-phase fractionation of human plasma samples followed by the quantitative analysis of specific fractions using nanoLC-parallel reaction monitoring (PRM) on a Q Exactive Plus mass spectrometer for peptide detection and quantitation with increased sensitivity. Because we use a set of synthetic peptide standards, we can more efficiently determine the precise retention times of the target peptides in the first-dimensional separation and specifically collect eluting fractions of interest for the subsequent targeted MS quantitation, making the analysis faster and easier. An eight-point standard curve was generated by serial dilution of a mixture of previously validated unlabeled ("light") synthetic peptides of interest at known concentrations. The corresponding heavy stable-isotope-labeled standard (SIS) analogues were used as normalizers to account for losses during sample processing and analysis. Using this method, we were able to improve the sensitivity of plasma protein quantitation by up to 50-fold compared to using nanoLC-PRM alone.

Bushfire exposure is associated with increased pH and dark-cutting in beef longissimus thoracis at grading.

To investigate if bushfire exposure is associated with increased loin pH, this study analysed temporal and geospatial data on fire incidence in South-Eastern Australia together with beef carcase quality and production records for fire affected animals (n = 451,299). Two outcomes were modelled: 1) loin pH at time of grading, and 2) the incidence of "high pH" defects (pH > 5.70). For both models, decreasing "time since closest fire" and "distance of property from closest fire" were associated with increasing loin pH and increased incidence of high pH carcases(p < 0.05 for all); interactions for "distance from the closest fire" with feed type (grain vs grass) and "days of fire exposure" with HGP (hormonal growth promotant) treatment (yes vs no) (p < 0.05 for both) indicate high pH outcomes were exacerbated in grass-fed and HGP treated cattle. It is concluded that exposure to bushfire is associated with increasing pH but the extent and magnitude of these increases are modulated by production factors.

Electrolyzed-Reduced Water: Review II: Safety Concerns and Effectiveness as a Source of Hydrogen Water.

Many studies demonstrate the safety of alkaline-electrolyzed-reduced water (ERW); however, several animal studies have reported significant tissue damage and hyperkalemia after drinking ERW. The mechanism responsible for these results remains unknown but may be due to electrode degradation associated with the production of higher pH, in which platinum nanoparticles and other metals that have harmful effects may leach into the water. Clinical studies have reported that, when ERW exceeds pH 9.8, some people develop dangerous hyperkalemia. Accordingly, regulations on ERW mandate that the pH of ERW should not exceed 9.8. It is recommended that those with impaired kidney function refrain from using ERW without medical supervision. Other potential safety concerns include impaired growth, reduced mineral, vitamin, and nutrient absorption, harmful bacterial overgrowth, and damage to the mucosal lining causing excessive thirst. Since the concentration of H2 in ERW may be well below therapeutic levels, users are encouraged to frequently measure the H2 concentration with accurate methods, avoiding ORP or ORP-based H2 meters. Importantly, although, there have been many people that have used high-pH ERW without any issues, additional safety research on ERW is warranted, and ERW users should follow recommendations to not ingest ERW above 9.8 pH.

Highly sensitive and specific responses of shrimp gill cells to high pH stress based on single cell RNA-seq analysis.

High pH is one of the main stressors affecting the shrimp survival, growth, and physiology in aquaculture ponds, but the cellular and molecular mechanism responsible for high pH stress has not been elucidated in shrimp. In this study, the shrimp acid-base disturbance and gill cell alterations were significantly observed and then single cell RNA-sequencing (scRNA-seq) was performed to study the sensitive and specific responses of gill cells to high pH stress. Three main gill cell types, including pillar cells, hemocytes and septal cells were identified. By comparative scRNA-seq analysis between control and pH group, the pillar cell was regarded as the target cell type in response to high pH stress with the down-regulation of ammonia excretion and H+ transport related genes and up-regulation of immune related genes. Notedly, high pH resulted in the emergence of a new immune cell subcluster in pillar cells, with immune activation and stress defense states. Pseudotime analysis also showed that the pillar cells could transform into the functionally inhibited ion cell subclusters and functionally activated immune cell subclusters after high pH stress. Further, the regulatory network of pillar cell population was predicted by WGCNA and two transcription factors were identified. In conclusion, these results provide key insights into the shrimp gill cell-type-specific mechanisms underlying high pH stress response at a single-cell resolution.

Effect of immersion in low-pH solution on physicochemical properties of high-pH venison.

The color of venison observed at a high-pH is not preferred by consumers. However, the physicochemical properties of venison soaked in a low-pH solution to lower its high-pH are unknown. We investigated the effect of immersion in a low-pH solution on the physicochemical properties of a high-pH venison. The pH of M. longissimus thoracis from seven female wild deer (Cervus nippon) was measured and divided into normal-pH venison and high-pH venison groups. The a* and b* values for high-pH venison were lower than those for normal-pH venison before storage. There was no significant difference in the pH between high-pH venison immersed in a pH 4 solution and normal-pH venison stored. The drip loss of immersed high-pH venison was significantly lower than that of normal-pH venison and high-pH venison. Cooking loss and total loss were the lowest for normal-pH venison and the highest for immersed high-pH venison. The maximum load between normal-pH venison, high-pH venison, and immersed high-pH venison did not differ significantly. Our work showed that meat color became favorable by immersing high-pH venison in a solution of pH 4, followed by heating.

Feedlot Factors Influencing the Incidence of Dark Cutting in Australian Grain-Fed Beef.

It has been well-established that dark cutting (DC) is a multifactorial issue that is associated with numerous animal and management factors. However, there is limited understanding of the feedlot-based factors that contribute to the influence of DC. The aim of this study was to evaluate the effect of climate, animal, and feedlot factors on the incidence of pH non-compliance in Australian grain-fed cattle. For this study, feedlot and abattoir records from 142,228 individual cattle over a 1-year period were investigated. These data incorporated records from seven feedlots that consigned cattle to three abattoirs. The average incidence of DC in these carcasses was 2.8%. The production factors that were associated with increased risk of DC included feedlot, sex, hormone growth promotants (HGP), cattle health, and days on feed (DOF). Additionally, DC also increased by reduced solar radiation (SR, W/m2), lower wind speeds (WS, m/s), increased ambient temperature (TA, °C), higher rainfall, a higher average temperature-humidity index (THI), and increased duration of time above heat-load-index threshold of 86 (HLI ≥ 86) during the 7 days prior to feedlot departure. This study identified the feedlot factors that increase the risk of DC from a feedlot-management perspective.

Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing.

In large-scale quantitative mass spectrometry (MS)-based phosphoproteomics, isobaric labeling with tandem mass tags (TMTs) coupled with offline high-pH reversed-phase peptide chromatographic fractionation maximizes depth of coverage. To investigate to what extent limited sample amounts affect sensitivity and dynamic range of the analysis due to sample losses, we benchmarked TMT-based fractionation strategies against single-shot label-free quantification with spectral library-free data independent acquisition (LFQ-DIA), for different peptide input per sample. To systematically examine how peptide input amounts influence TMT-fractionation approaches in a phosphoproteomics workflow, we compared two different high-pH reversed-phase fractionation strategies, microflow (MF) and stage-tip fractionation (STF), while scaling the peptide input amount down from 12.5 to 1 µg per sample. Our results indicate that, for input amounts higher than 5 µg per sample, TMT labeling, followed by microflow fractionation (MF) and phospho-enrichment, achieves the deepest phosphoproteome coverage, even compared to single shot direct-DIA analysis. Conversely, STF of enriched phosphopeptides (STF) is optimal for lower amounts, below 5 µg/peptide per sample. As a result, we provide a decision tree to help phosphoproteomics users to choose the best workflow as a function of sample amount.