Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes.

Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.

Associations of vegetable and fruit intake with cognitive function and its decline: Two longitudinal studies.

OBJECTIVES: Previous studies suggested protective associations of vegetables and fruits (VF) intake with cognitive function, but evidence on specific types of VF was insufficient. METHODS: The current study included 4066 participants from 1997 to 2006 in the China Health and Nutrition Survey (CHNS) and 6170 participants from 2013 to 2020 in the Health and Retirement Study (HRS). Dietary intake (using 3-day 24-h dietary recalls in CHNS and food frequency questionnaire in HRS) and cognitive function (using the Telephone Interview for Cognitive Status-Modified, TICS-m) were measured. Linear mixed-effects models were used to estimate the beta coefficients (ß) and the 95% confidence intervals (CI) to evaluate the association of VF with cognitive function (z-score) and its decline. RESULTS: Highest intake of total VF was associated with better cognitive function and slower cognitive decline. Differences in cognitive function z-score between the highest and lowest tertiles of VF consumption were 0.039 (95% CI: 0.002, 0.076) for CHNS and 0.063 (95% CI: 0.026, 0.100) for HRS. The corresponding differences in annual cognitive decline were 0.011 (95% CI: 0.002, 0.021) and 0.012 (95% CI: 0.003, 0.020) units respectively. Vegetables and fruits showed independent associations with cognitive function and its decline. In specific VF subgroups, when comparing the highest to the lowest tertile intake, cruciferous vegetables (ß = 0.058, 95% CI: 0.017, 0.100 in CHNS and ß = 0.067, 95% CI: 0.032, 0.101 in HRS) and green leafy vegetables (ß = 0.036, 95% CI: -0.001, 0.073 in CHNS and ß = 0.082, 95% CI: 0.046, 0.117 in HRS) was associated with better cognitive function in both cohorts. Similarly, higher intake of dark-colored vegetables (ß = 0.019, 95% CI: 0.008, 0.030 for red/yellow vegetables in CHNS and ß = 0.004, 95% CI: 0.001, 0.007 for green leafy vegetables in HRS) were associated with slower cognitive decline in subsequent years. Moreover, rigorous sensitivity analyses confirmed the stability of the results. CONCLUSIONS: Our findings support the potential beneficial roles of VF, especially cruciferous vegetables, green leafy vegetables, and red/yellow vegetables, in maintaining cognitive function and slowing cognitive decline in middle-aged and older adults.

Maackia amurensis seed lectin (MASL) and soluble human podoplanin (shPDPN) sequence analysis and effects on human oral squamous cell carcinoma (OSCC) cell migration and viability.

Maackia amurensis lectins serve as research and botanical agents that bind to sialic residues on proteins. For example, M. amurensis seed lectin (MASL) targets the sialic acid modified podoplanin (PDPN) receptor to suppress arthritic chondrocyte inflammation, and inhibit tumor cell growth and motility. However, M. amurensis lectin nomenclature and composition are not clearly defined. Here, we sought to definitively characterize MASL and its effects on tumor cell behavior. We utilized SDS-PAGE and LC-MS/MS to find that M. amurensis lectins can be divided into two groups. MASL is a member of one group which is composed of subunits that form dimers, evidently mediated by a cysteine residue in the carboxy region of the protein. In contrast to MASL, members of the other group do not dimerize under nonreducing conditions. These data also indicate that MASL is composed of 4 isoforms with an identical amino acid sequence, but unique glycosylation sites. We also produced a novel recombinant soluble human PDPN receptor (shPDPN) with 17 threonine residues glycosylated with sialic acid moieties with potential to act as a ligand trap that inhibits OSCC cell growth and motility. In addition, we report here that MASL targets PDPN with very strong binding kinetics in the nanomolar range. Moreover, we confirm that MASL can inhibit the growth and motility of human oral squamous cell carcinoma (OSCC) cells that express the PDPN receptor. Taken together, these data characterize M. amurensis lectins into two major groups based on their intrinsic properties, clarify the composition of MASL and its subunit isoform sequence and glycosylation sites, define sialic acid modifications on the PDPN receptor and its ability to act as a ligand trap, quantitate MASL binding to PDPN with KD in the nanomolar range, and verify the ability of MASL to serve as a potential anticancer agent.

N-3-Methylbutyl-benzisoselenazol-3(2H)-one Exerts Antifungal Activity In Vitro and in a Mouse Model of Vulvovaginal Candidiasis.

In the present work, we evaluated the antifungal activities of two novel ebselen analogs, N-allyl-benzisoselenazol-3(2H)-one (N-allyl-bs) and N-3-methylbutylbenzisoselenazol-3(2H)-one (N-3mb-bs). Colorimetric and turbidity assays were performed to determine the minimum inhibitory concentration (MIC) of these compounds in S1 (fluconazole-sensitive) and S2 (fluconazole-resistant) strains of C. albicans. N-3mb-bs was more active than the N-allyl-bs compound. It is noteworthy that the concentration of N-3mb-bs observed to inhibit fungal growth by 50% (18.2 µM) was similar to the concentration observed to inhibit the activity of the yeast plasma membrane H+-ATPase (Pma1p) by 50% (19.6 µM). We next implemented a mouse model of vulvovaginal candidiasis (VVC) using the S1 strain and examined the mouse and yeast proteins present in the vaginal lavage fluid using proteomics. The yeast proteins detected were predominately glycolytic enzymes or virulence factors associated with C. albicans while the mouse proteins present in the lavage fluid included eosinophil peroxidase, desmocollin-1, and gasdermin-A. We then utilized the N-3mb-bs compound (12.5 mg/kg) in the mouse VVC model and observed that it significantly reduced the vaginal fungal burden, histopathological changes in vagina tissue, and expression of myeloperoxidase (MPO). All in all, the present work has identified a potentially promising drug candidate for VVC treatment.

Risk perception predicts post-traumatic growth during the COVID-19 pandemic in China: the mediation effect of engaging in health-protective behaviors.

The COVID-19 pandemic exposed the public to enormous health risks and induced wide-ranging impacts on people's mental health. Post-traumatic growth is a possible psychological benefits that may occur during struggling with the COVID-19 pandemic. This research explored 1) demographics differences on risk perception of COVID-19 pandemic, engagement in health-protective behavior and post-traumatic growth during the COVID-19 pandemic; and 2) the mediation effect of engaging in health-protective behaviors between risk perception and post-traumatic growth during the COVID-19 pandemic. Females showed a significant higher level of engagement in health-protective behaviors. People who were married reported a significantly higher level of risk perception, engagement in health-protective behavior and post-traumatic growth than those who were in other marital status (i.e. single, divorced, widowed). People who had acquaintances being infected with COVID-19 reported significant higher level of risk perception and engagement in health-protective behaviors. Engagement in health-protective behaviors mediated the relationship between risk perception and post-traumatic growth. Implications of the results for public health interventions are discussed.

Degradation of sulfanilamide in aqueous solution by ionizing radiation: Performance and mechanism.

Sulfonamide (SA) is an emerging contaminants and the efficient treatment of SA containing wastewater remains a challenge. Herein, SA degradation by gamma irradiation has been systematacially studied. SA (10 mg/L) could be totally removed with 1.5 kGy irradiation. Quenching experiments demonstrated that •OH and eaq- were the predominant for SA degradation. SA degradation was reduced with initial concentration increasing, and the removal was faster with pH increasing in the range of 3.1-10.8. The coexisting matters affected SA degradation through changing reactive species, and the introduction of SO42- and Cl- enhanced SA degradation, while CO32- had a negative impact on SA degradation, and the degradation was insignificantly affected when adding humic acid. Gamma irradiation could remain effective in real water matrixes. In conjunction with LC-MS analysis and DFT calculation, possible degradation pathways for SA were proposed. Gamma irradiation could reduce the toxicity of SA, while several byproducts with more toxic were also formed. Furthermore, gamma/priodate (PI) process was promising to enhance SA degradation and mineralization. k value increased by 1.85 times, and mineralization rate increased from 19.51% to 79.19% when adding PI. This study suggested that ionizing radiation was efficient to eliminate SA in wastewater.

KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells.

Histone acetyltransferases KAT2A and KAT2B are paralogs highly expressed in the intestinal epithelium, but their functions are not well understood. In this study, double knockout of murine Kat2 genes in the intestinal epithelium was lethal, resulting in robust activation of interferon signaling and interferon-associated phenotypes including the loss of intestinal stem cells. Use of pharmacological agents and sterile organoid cultures indicated a cell-intrinsic double-stranded RNA trigger for interferon signaling. Acetyl-proteomics and dsRIP-seq were employed to interrogate the mechanism behind this response, which identified mitochondria-encoded double-stranded RNA as the source of intrinsic interferon signaling. Kat2a and Kat2b therefore play an essential role in regulating mitochondrial functions as well as maintaining intestinal health.

Mediterranean-Dietary Approaches to Stop Hypertension Intervention for Neurodegenerative Delay (MIND) Diet and Cognitive Function and its Decline: A Prospective Study and Meta-analysis of Cohort Studies.

BACKGROUND: Evidence on the association of the Mediterranean-Dietary Approaches to Stop Hypertension Intervention for Neurodegenerative Delay (MIND) diet with cognitive aging is limited and inconsistent. OBJECTIVES: We examined how the MIND diet is related to cognitive function and its decline among middle-aged and older adults. METHODS: We included 4066 participants with baseline dietary assessment and ≥1 cognitive test from the China Health and Nutrition Survey in 1997, 2000, 2004, and 2006, with a median follow-up of 3 y. The modified MIND diet score (range: 0-12) was calculated based on 9 healthy and 3 unhealthy food groups. Linear mixed-effect models were used to examine the association of adherence to the MIND diet with z-scores of cognitive function and cognitive decline. We also conducted a meta-analysis including our findings and 7 other cohort studies. RESULTS: At baseline, the median MIND diet scores across increasing tertile were 3.0, 4.0, and 5.5, respectively. Participants with higher MIND diet scores had better global cognitive function. The adjusted difference in global cognitive function z-score for every 3-point increment of MIND diet scores was 0.110 [95% confidence interval (CI), 0.060, 0.159, P-trend < 0.001], which was approximately equivalent to being 1 y younger in age. Consumption of nuts, fish, red meats, and tea showed independent positive associations with cognitive function, while fried food consumption exhibited inverse associations. In the meta-analysis of 26,103 participants, one standardized deviation increment of the MIND score was associated with 0.042 (95% CI: 0.020, 0.065) units higher in global cognitive function z-score and 0.010 (95% CI: -0.001, 0.021) units slower in annual cognitive decline. CONCLUSIONS: Our findings suggest that higher adherence to the MIND diet was associated with better cognitive function and potentially slower cognitive decline in later life. Further large-scale observational and interventional studies are warranted to elucidate the cognitive effects of the MIND diet. This meta-analysis was registered at PROSPERO as CRD42022330417.

A Therapeutically Targetable NOTCH1-SIRT1-KAT7 Axis in T-cell Leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is a NOTCH1-driven disease in need of novel therapies. Here, we identify a NOTCH1-SIRT1-KAT7 link as a therapeutic vulnerability in T-ALL, in which the histone deacetylase SIRT1 is overexpressed downstream of a NOTCH1-bound enhancer. SIRT1 loss impaired leukemia generation, whereas SIRT1 overexpression accelerated leukemia and conferred resistance to NOTCH1 inhibition in a deacetylase-dependent manner. Moreover, pharmacologic or genetic inhibition of SIRT1 resulted in significant antileukemic effects. Global acetyl proteomics upon SIRT1 loss uncovered hyperacetylation of KAT7 and BRD1, subunits of a histone acetyltransferase complex targeting H4K12. Metabolic and gene-expression profiling revealed metabolic changes together with a transcriptional signature resembling KAT7 deletion. Consistently, SIRT1 loss resulted in reduced H4K12ac, and overexpression of a nonacetylatable KAT7-mutant partly rescued SIRT1 loss-induced proliferation defects. Overall, our results uncover therapeutic targets in T-ALL and reveal a circular feedback mechanism balancing deacetylase/acetyltransferase activation with potentially broad relevance in cancer. SIGNIFICANCE: We identify a T-ALL axis whereby NOTCH1 activates SIRT1 through an enhancer region, and SIRT1 deacetylates and activates KAT7. Targeting SIRT1 shows antileukemic effects, partly mediated by KAT7 inactivation. Our results reveal T-ALL therapeutic targets and uncover a rheostat mechanism between deacetylase/acetyltransferase activities with potentially broader cancer relevance. This article is highlighted in the In This Issue feature, p. 1.

Independent effects of Src kinase and podoplanin on anchorage independent cell growth and migration.

The Src tyrosine kinase is a strong tumor promotor. Over a century of research has elucidated fundamental mechanisms that drive its oncogenic potential. Src phosphorylates effector proteins to promote hallmarks of tumor progression. For example, Src associates with the Cas focal adhesion adaptor protein to promote anchorage independent cell growth. In addition, Src phosphorylates Cas to induce Pdpn expression to promote cell migration. Pdpn is a transmembrane receptor that can independently increase cell migration in the absence of oncogenic Src kinase activity. However, to our knowledge, effects of Src kinase activity on anchorage independent cell growth and migration have not been examined in the absence of Pdpn expression. Here, we analyzed the effects of an inducible Src kinase construct in knockout cells with and without exogenous Pdpn expression on cell morphology migration and anchorage independent growth. We report that Src promoted anchorage independent cell growth in the absence of Pdpn expression. In contrast, Src was not able to promote cell migration in the absence of Pdpn expression. In addition, continued Src kinase activity was required for cells to assume a transformed morphology since cells reverted to a nontransformed morphology upon cessation of Src kinase activity. We also used phosphoproteomic analysis to identify 28 proteins that are phosphorylated in Src transformed cells in a Pdpn dependent manner. Taken together, these data indicate that Src utilizes Pdpn to promote transformed cell growth and motility in complementary, but parallel, as opposed to serial, pathways.

CK2 Inhibits TIMELESS Nuclear Export and Modulates CLOCK Transcriptional Activity to Regulate Circadian Rhythms.

Circadian clocks orchestrate daily rhythms in organismal physiology and behavior to promote optimal performance and fitness. In Drosophila, key pacemaker proteins PERIOD (PER) and TIMELESS (TIM) are progressively phosphorylated to perform phase-specific functions. Whereas PER phosphorylation has been extensively studied, systematic analysis of site-specific TIM phosphorylation is lacking. Here, we identified phosphorylation sites of PER-bound TIM by mass spectrometry, given the importance of TIM as a modulator of PER function in the pacemaker. Among the 12 TIM phosphorylation sites we identified, at least two of them are critical for circadian timekeeping as mutants expressing non-phosphorylatable mutations exhibit altered behavioral rhythms. In particular, we observed that CK2-dependent phosphorylation of TIM(S1404) promotes nuclear accumulation of PER-TIM heterodimers by inhibiting the interaction of TIM and nuclear export component, Exportin 1 (XPO1). We propose that proper level of nuclear PER-TIM accumulation is necessary to facilitate kinase recruitment for the regulation of daily phosphorylation rhythm and phase-specific transcriptional activity of CLOCK (CLK). Our results highlight the contribution of phosphorylation-dependent nuclear export of PER-TIM heterodimers to the maintenance of circadian periodicity and identify a new mechanism by which the negative elements of the circadian clock (PER-TIM) regulate the positive elements (CLK-CYC). Finally, because the molecular phenotype of tim(S1404A) non-phosphorylatable mutant exhibits remarkable similarity to that of a mutation in human timeless that underlies familial advanced sleep phase syndrome (FASPS), our results revealed an unexpected parallel between the functions of Drosophila and human TIM and may provide new insights into the molecular mechanisms underlying human FASPS.

Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings.

MAIN CONCLUSION: AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.

γ-ray induced formation of oxygen vacancies and Ti3+ defects in anatase TiO2 for efficient photocatalytic organic pollutant degradation.

Oxygen vacancies and Ti3+ defects in anatase TiO2 have attracted great attention to address the insufficient optical absorption and photoinduced charge-carrier separation in photocatalysis. In this study, we demonstrate a superficial and innovative approach for synthesizing anatase TiO2 nanoparticles with abundant oxygen vacancies via γ-ray irradiation reduction at room temperature. X-ray photoelectron spectroscopy (XPS) and electron paramagnetic resonance (EPR) confirm that oxygen vacancies and Ti3+ defects can be quantitatively and extensively obtained by merely regulating the irradiation dosage. Photoelectrochemical measurements suggest that oxygen vacancies and Ti3+ defects promoted the separation of electron-hole pairs and then enhanced the photocatalytic degradation performance for organic pollutant. In comparison with TiO2 (no irradiation), the sample (49.5 kGy irradiation) exhibited a 20.0-fold enhancement in visible-light decomposition of phenol. In addition, the results of scavenge experiments and mechanism analysis revealed that O2- are the dominant active species. The excited electrons generated at the conduction band and oxygen vacancy level of TiO2-x-49.5 conspicuously contributes to generate much more ·O2- species. This novel study shows at room temperature, the γ-ray approach of irradiation leads to faster formation and quantification of oxygen vacancies in the semiconductor materials.

Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics.

Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic range compared to TMT-MS3, MS1, and DIA, which were similar. Using a protein clustering approach to evaluate data quality by assignment of reference proteins to their correct compartments, all methods performed well, with isobaric labeling approaches providing the highest quality localization. Finally, TMT-MS2 gave the lowest percentage of missing quantifiable data when analyzing orthogonal fractionation methods containing overlapping proteomes. In summary, despite inaccuracies resulting from ratio compression, data obtained by TMT-MS2 assigned protein localization as well as other methods but achieved the highest proteome coverage with the lowest proportion of missing values.

Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome.

Treatments are emerging for the neuronal ceroid lipofuscinoses (NCLs), a group of similar but genetically distinct lysosomal storage diseases. Clinical ratings scales measure long-term disease progression and response to treatment but clinically useful biomarkers have yet to be identified in these diseases. We have conducted proteomic analyses of brain and cerebrospinal fluid (CSF) from mouse models of the most frequently diagnosed NCL diseases: CLN1 (infantile NCL), CLN2 (classical late infantile NCL) and CLN3 (juvenile NCL). Samples were obtained at different stages of disease progression and proteins quantified using isobaric labeling. In total, 8303 and 4905 proteins were identified from brain and CSF, respectively. We also conduced label-free analyses of brain proteins that contained the mannose 6-phosphate lysosomal targeting modification. In general, we detect few changes at presymptomatic timepoints but later in disease, we detect multiple proteins whose expression is significantly altered in both brain and CSF of CLN1 and CLN2 animals. Many of these proteins are lysosomal in origin or are markers of neuroinflammation, potentially providing clues to underlying pathogenesis and providing promising candidates for further validation.

Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation.

The ubiquitin system is crucial for the development and fitness of higher plants. De-etiolation, during which green plants initiate photomorphogenesis and establish autotrophy, is a dramatic and complicated process that is tightly regulated by a massive number of ubiquitylation/de-ubiquitylation events. Here we present site-specific quantitative proteomic data for the ubiquitylomes of de-etiolating seedling leaves of Zea mays L. (exposed to light for 1, 6, or 12 h) achieved through immunoprecipitation-based high-resolution mass spectrometry (MS). Through the integrated analysis of multiple ubiquitylomes, we identified and quantified 1926 unique ubiquitylation sites corresponding to 1053 proteins. We analyzed these sites and found five potential ubiquitylation motifs, KA, AXK, KXG, AK, and TK. Time-course studies revealed that the ubiquitylation levels of 214 sites corresponding to 173 proteins were highly correlated across two replicate MS experiments, and significant alterations in the ubiquitylation levels of 78 sites (fold change >1.5) were detected after de-etiolation for 12 h. The majority of the ubiquitylated sites we identified corresponded to substrates involved in protein and DNA metabolism, such as ribosomes and histones. Meanwhile, multiple ubiquitylation sites were detected in proteins whose functions reflect the major physiological changes that occur during plant de-etiolation, such as hormone synthesis/signaling proteins, key C4 photosynthetic enzymes, and light signaling proteins. This study on the ubiquitylome of the maize seedling leaf is the first attempt ever to study the ubiquitylome of a C4 plant and provides the proteomic basis for elucidating the role of ubiquitylation during plant de-etiolation.

Optimization of flocculation conditions for soluble cadmium removal using the composite flocculant of green anion polyacrylamide and PAC by response surface methodology.

In this work, we describe a flocculation performance evaluation of a novel anionic polyacrylamide (APAM) synthesized using low dose γ-ray initiation. The APAM structure and morphology were characterized using Fourier transform-infrared spectroscopy (FTIR), High performance liquid chromatography (HPLC), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM) techniques. In comparison to commercially purchased APAM (Mw = 1.0 × 107), γ-ray initiation was demonstrated to be a more effective method to increase molecular weight, decrease the residual acrylamide monomer, and improve thermal stability. Flocculant performance was evaluated by assessing their ability to remove Cd(II) from water. We utilized the Plackett-Burman (PB), steepest ascent, and response surface methodology (RSM) experimental design to identify the optimal flocculating conditions for the removal of soluble Cd(II). Under optimal conditions [26.84 mg L-1 CaO, 71.28 mg L-1 polyaluminium chloride (PAC) and 2.87 mg L-1 APAM], the maximum percent removal of Cd(II) was observed to reach 93.65%. A potential flocculation mechanism for the Cd(II) removal from water was further studied by evaluating the colloid Zeta potential. Results from these studies demonstrated that PAC had a greater capability to change the Zeta potential of collide under alkaline conditions, while APAM played a critical role in the bridging, enmeshment, and sweeping effect. The composite of two types of predominance makes considerable sense in regards to enhancing flocculating efficiency, decreasing secondary pollution, and reducing flocculant cost.

Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers.

Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To identify candidate biomarkers, we analyzed autopsy brain and matching CSF samples from controls and three genetically distinct NCLs due to deficiencies in palmitoyl protein thioesterase 1 (CLN1 disease), tripeptidyl peptidase 1 (CLN2 disease), and CLN3 protein (CLN3 disease). Proteomic and biochemical methods were used to analyze lysosomal proteins, and, in general, we find that changes in protein expression compared with control were most similar between CLN2 disease and CLN3 disease. This is consistent with previous observations of biochemical similarities between these diseases. We also conducted unbiased proteomic analyses of CSF and brain using isobaric labeling/quantitative mass spectrometry. Significant alterations in protein expression were identified in each NCL, including reduced STXBP1 in CLN1 disease brain. Given the confounding variable of post-mortem changes, additional validation is required, but this study provides a useful starting set of candidate NCL biomarkers for further evaluation.

Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome.

Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle whereas a significant fraction may reside elsewhere. As a step toward a comprehensive cellular map, we used subcellular fractionation with classic balance sheet analysis and isobaric labeling/quantitative mass spectrometry to assign locations to >6000 rat liver proteins. We provide quantitative data and error estimates describing the distribution of each protein among the eight major cellular compartments: nucleus, mitochondria, lysosomes, peroxisomes, endoplasmic reticulum, Golgi, plasma membrane and cytosol. Accounting for total intracellular distribution improves quality of organelle assignments and assigns proteins with multiple locations. Protein assignments and supporting data are available online through the Prolocate website (http://prolocate.cabm.rutgers.edu). As an example of the utility of this data set, we have used organelle assignments to help analyze whole exome sequencing data from an infant dying at 6 months of age from a suspected neurodegenerative lysosomal storage disorder of unknown etiology. Sequencing data was prioritized using lists of lysosomal proteins comprising well-established residents of this organelle as well as novel candidates identified in this study. The latter included copper transporter 1, encoded by SLC31A1, which we localized to both the plasma membrane and lysosome. The patient harbors two predicted loss of function mutations in SLC31A1, suggesting that this may represent a heretofore undescribed recessive lysosomal storage disease gene.