Hot Phenol Method Research Articles

Preparation and evaluation of a new combined conjugated vaccine against Klebsiella pneumonia and Pseudomonas aeruginosa

Lower respiratory tract infections (LRTIs) have been identified by the World Health Organization as the most deadly infectious diseases and a pervasive public health problem, causing increased hospital admissions, mortality and antibiotic use. This study aims to determine the most common and resistant bacteria that cause LRTIs and prepare an appropriate vaccine to reduce and prevent potential future infections. Our survey was conducted by collecting respiratory exudate specimens. The most predominant and resistant types were Klebsiella pneumonia and Pseudomonas aeruginosa. The lipopolysaccharides (LPS) were extracted using a modified hot phenol method to prepare the vaccine. The LPS were then activated and conjugated. The immunogenicity of the prepared singles and combined vaccines was determined through an in vivo assay using BALB/c mice. The prepared vaccine provided high protection against the lethal dose of both bacteria in mice. The combined vaccine shows a significant value in achieving high immunization. These findings demonstrate the potential of the bacterial LPS molecules to be used as effective vaccines. Developing an effective single and combined vaccine against P. aeruginosa and K. pneumonia can protect and reduce LRTI incidence.

Extraction and Characterization of Lipopolysaccharide from Salmonella typhi

There is no standard process available for high purity LPS isolation, and it may be appropriate to mix two purification steps. For Salmonella typhi LPS that were subjected to normal microbiological & biochemical screening protocols, updated phenol-water extraction protocol & non-phenolic extraction methods were also used in present research. Pellet of crude LPS obtained with wet weight was 2.0 gm. yield of LPS was more by hot phenol method 1.94 mg/ml as compared to non-phenolic method 0.40 mg/ml. relative purity of LPS obtained by hot phenol method was more as compared to non-phenolic method, as protein content was 23.60 mg/ml in LPS extracted from hot phenol method & 26.62 mg/ ml in LPS extracted from non-phenolic method. However, Nucleic acid contain was comparable in LPS extracted from both methods. Qualitative analysis showed ladder like bands of LPS extracted by hot phenol method as compared to single band obtained for LPS extracted by non-phenolic method. Findings of silver staining clearly revealed ladder pattern of multi-rung bands that are characteristics of smooth form of gram negative bacteria due to difference in length of carbohydrate chain of O-antigen component. In order to clarify diseased conditions & better work on LPS profiling, this research may be crucial to lead to more successful diagnosis and care.

A Simple Method for Extraction of Lipopolysaccharides from Brucella Melitensis

Background: Brucellosis is the most common zoonotic bacterial disease around the world, and its causative agent is Brucella, a gram-negative bacterium. Lipopolysaccharide (LPS) molecules are the most significant surface antigen of Brucella bacteria. This antigen is used in a high number of research and diagnostic fields. The present study was designed in order to introduce a simple method to extract LPS from Brucella melitensis. Materials and Methods: Smooth strains of B. melitensis were cultured in large quantity, and LPS was extracted through changes in the hot-phenol method. The LPS concentration was measured by using the dimethyl-methylene blue method. The contamination rates of proteins and nucleic acids were determined using the bicinchoninic acid (BCA) method and absorbance measurement at 260 nm, respectively. Results: The amount of the extracted LPS was 1.1% of the wet weight of the bacteria. The rate of contamination with nucleic acid was measured to be 0.2% of the LPS. The protein contamination was not detectable through the BCA method. Conclusion: The advantages of our newly-introduced method are considerable decrease in the time required to extract LPS; independence from nucleic acid and protein digestive enzymes; an extraction rate of LPS equivalent to other applied methods; nucleic acid contamination equal or lower than other methods, and no protein contamination; and independence from equipment such as ultracentrifuge and chromatography. [GMJ.2021;10:e1944]

A Simple Method for Extraction of Lipopolysaccharides from Brucella Melitensis

Background: Brucellosis is the most common zoonotic bacterial disease around the world, and its causative agent is Brucella, a gram-negative bacterium. Lipopolysaccharide (LPS) molecules are the most significant surface antigen of Brucella bacteria. This antigen is used in a high number of research and diagnostic fields. The present study was designed in order to introduce a simple method to extract LPS from Brucella melitensis. Materials and Methods: Smooth strains of B. melitensis were cultured in large quantity, and LPS was extracted through changes in the hot-phenol method. The LPS concentration was measured by using the dimethyl-methylene blue method. The contamination rates of proteins and nucleic acids were determined using the bicinchoninic acid (BCA) method and absorbance measurement at 260 nm, respectively. Results: The amount of the extracted LPS was 1.1% of the wet weight of the bacteria. The rate of contamination with nucleic acid was measured to be 0.2% of the LPS. The protein contamination was not detectable through the BCA method. Conclusion: The advantages of our newly-introduced method are considerable decrease in the time required to extract LPS; independence from nucleic acid and protein digestive enzymes; an extraction rate of LPS equivalent to other applied methods; nucleic acid contamination equal or lower than other methods, and no protein contamination; and independence from equipment such as ultracentrifuge and chromatography. [GMJ.2021;10:e1944]

Cytotoxicity of lipopolysaccharide extracted from Salmonella enterica serovar Typhimurium on Breast Cancer Cell Line mcf-7

Lipopolysaccharide was selected to investigate its effect on cell line of breast cancer in vitro, thereforelipopolysaccharide was extract from Salmonella enterica serovar Typhimurium followed by evaluation of itscytotoxicity. The experiment was divided into three parts. The first part included isolation and identificationof S. enterica serovar Typhimurium from 302 samples included 201diarrheic patient samples and 101 foodsamples of poultry meat and as well as the isolates identification on molecular level through used of threegenes (invA, STM4497 and Stn) genes detected using the technique of PCR, the results shown there wereseven bacterial isolates diagnosed as S. enterica serovar Typhimurium. The second part of the experimentwas extract of LPS from 10.66 g of dry weight of bacteria by hot phenol method. The concentration of LPSin phenolic phase was 435.57?g/ml while in aqueous phase was 381.76 ?g/ml. The LPS molecular weightwas estimate which was equivalent to 93325 for phenolic and 71614 Dalton for aqueous phases. The thirdpart of experiment was to study the effect of cytotoxicity in cell line of breast cancer by used differentconcentrations of lipopolysaccharide. Lipopolysaccharide showed cytotoxicity on the breast cancer cell linemcf-7 in both phenolic and aqueous phases of LPS. The results showed the highest rate of inhibition ofbreast cancer cells at the concentration of 350 ?g/ml by 61.67% in the phenolic phase while the rate ofinhibition was 53.33% in the same concentration of the aqueous phase.

Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria.

Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are involved in gene expression regulation. Taken into account the classical gene structure, we are able to identify two kinds of transcriptional start site: primary and secondary. A primary transcriptional start site is located some nucleotides upstream of the translational start site, while a secondary transcriptional start site is located within the gene encoding sequence. Here, we present a step by step protocol for genome-wide transcriptional start sites determination by differential RNA-sequencing (dRNA-seq) using the enteric pathogen Shigella flexneri serotype 5a strain M90T as model. However, this method can be employed in any other bacterial species of choice. In the first steps, total RNA is purified from bacterial cultures using the hot phenol method. Ribosomal RNA (rRNA) is specifically depleted via hybridization probes using a commercial kit. A 5'-monophosphate-dependent exonuclease (TEX)-treated RNA library enriched in primary transcripts is then prepared for comparison with a library that has not undergone TEX-treatment, followed by ligation of an RNA linker adaptor of known sequence allowing the determination of TSS with single nucleotide precision. Finally, the RNA is processed for Illumina sequencing library preparation and sequenced as purchased service. TSS are identified by in-house bioinformatic analysis. Our protocol is cost-effective as it minimizes the use of commercial kits and employs freely available software.

An Efficient Method for High Quality RNA Extraction from Moringa oleifera

Moringa oleifera, the Miracle Tree is rich in all nutrients and minerals. It has prominent distribution of secondary metabolites like polysaccharides, phenols and mucilage, which makes extraction of RNA quite difficult. A high quality and pure RNA is prerequisite for the study of high through put transcriptomics and functional genomics. A protocol for isolation of highly qualitative and quantitative RNA from M. oleifera was optimized by comparing five different methods like Trizol, Guanidine hydrochloride, combined Trizol and Guanidine hydrochloride, modified CTAB and hot phenol method. The combined Guanidine hydrochloride and Trizol method gave good yield and pure RNA based on the absorbance A260 value 2.0. The model plant Nicotiana tabacum served as a positive control in which the Trizol method yielded a good quality and quantity RNA. The present study is a preliminary step for studying the function and expression pattern of the genes. This is the first report on the comparison of different RNA extraction methods in M. oleifera to our knowledge.

Purification and antigenic detection of O-specific polysaccharides of Salmonella enterica serovar Paratyphi A isolate from Pakistan: an emerging threat.

BackgroundParatyphoid fever caused by Salmonella enterica serovar Paratyphi A is becoming a serious health problem in Asian countries particularly Pakistan, China and India and situation is aggravated by current unavailability of a licensed vaccine. This study was designed to purify the O-specific polysaccharides (OSP) produced by an isolate of Salmonella Paratyphi A from Pakistan and detect antigenicity of extracted lipopolysaccharide (LPS) and purified OSP pioneerly in South Asian region as candidate for conjugate vaccine preparation.Results S. Paratyphi A isolates were identified through PCR using primers of fliC-a gene (329 bp) and confirmed via nested PCR using fliC-nested primers (289 bp). Yield of the LPS of S. Paratyphi A isolate was 40 mg/L of the bacterial culture using hot phenol method. The purified LPS revealed the characteristic ladder like pattern of S. Paratyphi A LPS on SDS-PAGE with silver staining. Purified OSP obtained by acid hydrolysis yielded 23 mg/L of culture broth and was not detected by silver staining. Antigenic interaction of the purified LPS and OSP with hyper immune mice sera was confirmed by single precipitin line evaluated through immunodiffusion assay. The antigenicity was found well intact.ConclusionsThe purified antigenic OSP from S. Paratyphi A may have the potential to be coupled with a carrier protein to develop low cost conjugate vaccine candidates against S. Paratyphi A in paratyphoid endemic regions.

Simplest identification, O-specific polysaccharide purification and antigenic evaluation of Salmonella enterica serovar Typhi Vi negative isolate.

Currently licensed typhoid vaccines are based on Vi capsular polysaccharides. Recent molecular reports from typhoid endemic countries state that Salmonella enterica serovar Typhi (S. Typhi) Vi negative strains occur naturally and cause typhoid fever which is indistinguishable from disease caused by Vi positive strains. Vaccine based on Vi polysaccharide may not protect patients if the invading S. Typhi are negative for Vi. The lipopolysaccharide (LPS) is an essential component of S. Typhi outer membrane in which O-specific polysaccharide (OSP) is a protective antigen and universal candidate for vaccine development. In this study, S. Typhi Vi negative isolates were discriminated from Vi positive isolates through a duplex PCR using primers of fliC-d (599bp) and tviA (495bp) genes. The LPS of S. Typhi Vi negative isolates was extracted by hot phenol method and OSP was purified by core hydrolysis. The yield of extracted LPS was 91 mg/L and that of purified OSP was 49.14 mg/L of culture broth. LPS showed ladder like appearance by zinc imidazole staining following SDS-PAGE. Whole cell challenged mice sera were used for in vitro antigenicity evaluation of the purified LPS and OSP. The antigenicity was found adequate by immunodiffusion assay. To our knowledge, this is the first report of purification and antigenic evaluation of LPS of a Vi negative S. Typhi isolate. The purified OSP from S. Typhi Vi negative isolate may be coupled with a carrier protein to produce universal low cost conjugate vaccine candidates for use in typhoid endemic regions.

Impact of RNA isolation protocols on RNA detection by Northern blotting.

We prepared total RNA from the Gram-positive soil bacterium Bacillus subtilis by different RNA extraction procedures to compare their suitability for Northern blot detection of tiny RNAs (~14-mers) or RNAs of intermediate size (100-200 nt) in terms of signal quality, intensity, and reproducibility. Our analysis included two hot phenol methods and two TRIzol extraction procedures. We found that signal intensity/detection sensitivity makes the key difference. Total RNAs prepared by the hot phenol method comprise the length spectrum from tRNAs to large ribosomal RNAs. Larger RNAs are less abundant in TRIzol preparations which instead enrich for RNAs of tRNA size and smaller. Thus, hot phenol methods are the choice for the detection of intermediate-sized and longer RNAs, whereas TRIzol extraction procedures are more suited for the detection of tiny RNAs.

Extraction and Purification of Haemophilus influenzae Type b Lipooligosac‌charide by Modified Phenol Method

Introduction: Haemophilus influenzae type b (Hib) is a Gram negative bacterium and one of the causative agents of acute bacterial meningitis, especially in infants and children less than 5 years old. Lipooligosaccharide (LOS), one of the virulence factors which plays an important role in pathogenesis of Hib, has multiple applications in diagnosis and conjugate vaccines. In this study, LOS extracted from two Hib standard strains (ATCC 39930 and ATCC 10214) were compared. Methods: LOS was extracted by a modified hot phenol method from the aqueous and phenol phase and its concentration and purity assayed. Protein contaminations of the samples were determined spectrophotometrically and their endotoxin contents were assayed by the Limulus amebocyte lysate (LAL). Result: The yield of the extracted LOS from strain ATCC10214 was about 475 μg/ml and the protein contaminations of the samples were approximately 0.07 mg/ml, whereas strain ATCC39930 yielded 520 μg/ ml of LOS with protein contamination of 0.08 mg/ml. The results showed that the production of LOS by both strains was similar and the variation observed was not statistically significant (p < 0.001). Vac Res, 2014, 1 (1): 28-30

Enhancement of HIV-1 DNA vaccine immunogenicity by BCG-PSN, a novel adjuvant

Although the importance of DNA vaccines, especially as a priming immunization has been well established in numerous HIV vaccine studies, the immunogenictiy of DNA vaccines is generally moderate. Novel adjuvant is in urgent need for improving the immunogenicity of DNA vaccine. Polysaccharide and nucleic acid fraction extracted by hot phenol method from Mycobacterium bovis bacillus Calmette-Guérin, known as BCG-PSN, is a widely used immunomodulatory product in China clinical practice. In this study, we evaluated whether the BCG-PSN could serve as a novel adjuvant of DNA vaccine to trigger better cellular and humoral immune responses against the HIV-1 Env antigen in Balb/C mouse model. The BCG-PSN was mixed with 10μg or 100μg of pDRVI1.0gp145 (HIV-1 CN54 gp145 gene) DNA vaccine and intramuscularly immunized two or three times. We found that BCG-PSN could significantly improve the immunogenicity of DNA vaccine when co-administered with DNA vaccine. Further, at the same vaccination schedule, BCG-PSN co-immunization with 10μg DNA vaccine could elicit cellular and humoral immune responses which were comparable to that induced by 100μg DNA vaccine alone. Moreover, our results demonstrate that BCG-PSN can activate TLR signaling pathways and induce Th1-type cytokines secretion. These findings suggest that BCG-PSN can serve as a novel and effective adjuvant for DNA vaccination.

Acetyl-CoA Carboxylase Regulates Global Histone Acetylation

Histone acetylation depends on intermediary metabolism for supplying acetyl-CoA in the nucleocytosolic compartment. However, because nucleocytosolic acetyl-CoA is also used for de novo synthesis of fatty acids, histone acetylation and synthesis of fatty acids compete for the same acetyl-CoA pool. The first and rate-limiting reaction in de novo synthesis of fatty acids is carboxylation of acetyl-CoA to form malonyl-CoA, catalyzed by acetyl-CoA carboxylase. In yeast Saccharomyces cerevisiae, acetyl-CoA carboxylase is encoded by the ACC1 gene. In this study, we show that attenuated expression of ACC1 results in increased acetylation of bulk histones, globally increased acetylation of chromatin histones, and altered transcriptional regulation. Together, our data indicate that Acc1p activity regulates the availability of acetyl-CoA for histone acetyltransferases, thus representing a link between intermediary metabolism and epigenetic mechanisms of transcriptional regulation.

Mfc1 Is a Novel Forespore Membrane Copper Transporter in Meiotic and Sporulating Cells

To gain insight in the molecular basis of copper homeostasis during meiosis, we have used DNA microarrays to analyze meiotic gene expression in the model yeast Schizosaccharomyces pombe. Profiling data identified a novel meiosis-specific gene, termed mfc1(+), that encodes a putative major facilitator superfamily-type transporter. Although Mfc1 does not exhibit any significant sequence homology with the copper permease Ctr4, it contains four putative copper-binding motifs that are typically found in members of the copper transporter family of copper transporters. Similarly to the ctr4(+) gene, the transcription of mfc1(+) was induced by low concentrations of copper. However, its temporal expression profile during meiosis was distinct to ctr4(+). Whereas Ctr4 was observed at the plasma membrane shortly after induction of meiosis, Mfc1 appeared later in precursor vesicles and, subsequently, at the forespore membrane of ascospores. Using the fluorescent copper-binding tracker Coppersensor-1 (CS1), labile cellular copper was primarily detected in the forespores in an mfc1(+)/mfc1(+) strain, whereas an mfc1Δ/mfc1Δ mutant exhibited an intracellular dispersed punctate distribution of labile copper ions. In addition, the copper amine oxidase Cao1, which localized primarily in the forespores of asci, was fully active in mfc1(+)/mfc1(+) cells, but its activity was drastically reduced in an mfc1Δ/mfc1Δ strain. Furthermore, our data showed that meiotic cells that express the mfc1(+) gene have a distinct developmental advantage over mfc1Δ/mfc1Δ mutant cells when copper is limiting. Taken together, the data reveal that Mfc1 serves to transport copper for accurate and timely meiotic differentiation under copper-limiting conditions.

Cap2-HAP Complex Is a Critical Transcriptional Regulator That Has Dual but Contrasting Roles in Regulation of Iron Homeostasis in Candida albicans

Iron homeostasis is highly regulated in organisms across evolutionary time scale as iron is essential for various cellular processes. In a computational screen, we identified the Yap/bZIP domain family in Candida clade genomes. Cap2/Hap43 is essential for C. albicans growth under iron-deprivation conditions and for virulence in mouse. Cap2 has an amino-terminal bipartite domain comprising a fungal-specific Hap4-like domain and a bZIP domain. Our mutational analyses showed that both the bZIP and Hap4-like domains perform critical and independent functions for growth under iron-deprivation conditions. Transcriptome analysis conducted under iron-deprivation conditions identified about 16% of the C. albicans ORFs that were differentially regulated in a Cap2-dependent manner. Microarray data also suggested that Cap2 is required to mobilize iron through multiple mechanisms; chiefly by activation of genes in three iron uptake pathways and repression of iron utilizing and iron storage genes. The expression of HAP2, HAP32, and HAP5, core components of the HAP regulatory complex was induced in a Cap2-dependent manner indicating a feed-forward loop. In a feed-back loop, Cap2 repressed the expression of Sfu1, a negative regulator of iron uptake genes. Cap2 was coimmunoprecipitated with Hap5 from cell extracts prepared from iron-deprivation conditions indicating an in vivo association. ChIP assays demonstrated Hap32-dependent recruitment of Hap5 to the promoters of FRP1 (Cap2-induced) and ACO1 (Cap2-repressed). Together our data indicates that the Cap2-HAP complex functions both as a positive and a negative regulator to maintain iron homeostasis in C. albicans.

Co-precipitation of Phosphate and Iron Limits Mitochondrial Phosphate Availability in Saccharomyces cerevisiae Lacking the Yeast Frataxin Homologue (YFH1)

Saccharomyces cerevisiae cells lacking the yeast frataxin homologue (Δyfh1) accumulate iron in the mitochondria in the form of nanoparticles of ferric phosphate. The phosphate content of Δyfh1 mitochondria was higher than that of wild-type mitochondria, but the proportion of mitochondrial phosphate that was soluble was much lower in Δyfh1 cells. The rates of phosphate and iron uptake in vitro by isolated mitochondria were higher for Δyfh1 than wild-type mitochondria, and a significant proportion of the phosphate and iron rapidly became insoluble in the mitochondrial matrix, suggesting co-precipitation of these species after oxidation of iron by oxygen. Increasing the amount of phosphate in the medium decreased the amount of iron accumulated by Δyfh1 cells and improved their growth in an iron-dependent manner, and this effect was mostly transcriptional. Overexpressing the major mitochondrial phosphate carrier, MIR1, slightly increased the concentration of soluble mitochondrial phosphate and significantly improved various mitochondrial functions (cytochromes, [Fe-S] clusters, and respiration) in Δyfh1 cells. We conclude that in Δyfh1 cells, soluble phosphate is limiting, due to its co-precipitation with iron.

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80°C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method.

Yeast Colony Survival Depends on Metabolic Adaptation and Cell Differentiation Rather Than on Stress Defense

Enzymes scavenging reactive oxygen species (ROS) are important for cell protection during stress and aging. A deficiency in these enzymes leads to ROS imbalance, causing various disorders in many organisms, including yeast. In contrast to liquid cultures, where fitness of the yeast population depends on its ROS scavenging capability, the present study suggests that Saccharomyces cerevisiae cells growing in colonies capable of ammonia signaling use a broader protective strategy. Instead of maintaining high levels of antioxidant enzymes for ROS detoxification, colonies activate an alternative metabolism that prevents ROS production. Colonies of the strain deficient in cytosolic superoxide dismutase Sod1p thus developed the same way as wild type colonies. They produced comparable levels of ammonia and underwent similar developmental changes (expression of genes of alternative metabolism and center margin differentiation in ROS production, cell death occurrence, and activities of stress defense enzymes) and did not accumulate stress-resistant suppressants. An absence of cytosolic catalase Ctt1p, however, brought colonies developmental problems, which were even more prominent in the absence of mitochondrial Sod2p. sod2Delta and ctt1Delta colonies failed in ammonia production and sufficient activation of the alternative metabolism and were incapable of center margin differentiation, but they did not increase ROS levels. These new data indicate that colony disorders are not accompanied by ROS burst but could be a consequence of metabolic defects, which, however, could be elicited by imbalance in ROS produced in early developmental phases. Sod2p and homeostasis of ROS may participate in regulatory events leading to ammonia signaling.

Is There a Link between the Lipopolysaccharide of Helicobacter pylori Gastric MALT Lymphoma Associated Strains and Lymphoma Pathogenesis?

The aim of this study was to investigate the Lewis antigen expression in Helicobacter pylori gastric MALT lymphoma associated strains in comparison to chronic gastritis only strains. Forty MALT strains (19 cagPAI (−) and 21 cagPAI (+)) and 39 cagPAI frequency-matched gastritis strains (17 cagPAI (−) and 22 cagPAI (+)) were included in this study. The lipopolyssacharide for each strain was extracted using a hot phenol method and the expression of Lex and Ley were investigated using Western Blot. The data were analyzed according to the strains' cagPAI status and vacA genotype. Lex was identified in 21 (52.5%) MALT strains and 29 (74.3%) gastritis strains. Ley was identified in 30 (75%) MALT strains and 31 (79.5%) gastritis strains. There was an association between cagPAI positivity and Lex expression among MALT strains (p<0.0001), but not in gastritis strains (p = 0.64). Among cagPAI (−) strains, isolates expressing solely Ley were associated with MALT with an odds ratio of 64.2 (95% CI 4.9–841.0) when compared to strains expressing both Lex and Ley. vacA genotypes did not modify the association between Lewis antigen expression and disease status. In conclusion, cagPAI (−) MALT strains have a particular Lewis antigen profile which could represent an adaptive mechanism to the host response or participate in MALT lymphomagenesis.

Transcriptional Activation in Yeast in Response to Copper Deficiency Involves Copper-Zinc Superoxide Dismutase

Copper is an essential trace element, yet excess copper can lead to membrane damage, protein oxidation, and DNA cleavage. To balance the need for copper with the necessity to prevent accumulation to toxic levels, cells have evolved sophisticated mechanisms to regulate copper acquisition, distribution, and storage. In Saccharomyces cerevisiae, transcriptional responses to copper deficiency are mediated by the copper-responsive transcription factor Mac1. Although Mac1 activates the transcription of genes involved in high affinity copper uptake during periods of deficiency, little is known about the mechanisms by which Mac1 senses or responds to reduced copper availability. Here we show that the copper-dependent enzyme Sod1 (Cu,Zn-superoxide dismutase) and its intracellular copper chaperone Ccs1 function in the activation of Mac1 in response to an external copper deficiency. Genetic ablation of either CCS1 or SOD1 results in a severe defect in the ability of yeast cells to activate the transcription of Mac1 target genes. The catalytic activity of Sod1 is essential for Mac1 activation and promotes a regulated increase in binding of Mac1 to copper response elements in the promoter regions of genomic Mac1 target genes. Although there is precedent for additional roles of Sod1 beyond protection of the cell from oxygen radicals, the involvement of this protein in copper-responsive transcriptional regulation has not previously been observed. Given the presence of both Sod1 and copper-responsive transcription factors in higher eukaryotes, these studies may yield important insights into how copper deficiency is sensed and appropriate cellular responses are coordinated.