Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptide‐nucleotide antibiotic Microcin C is a potent inducer of stringent response and persistence in both sensitive and producing cells

Microcin C (McC) is a peptide‐nucleotide antibiotic that inhibits aspartyl‐tRNA synthetase. Here, we show that McC is a strong inducer of persistence in Escherichia coli. Persistence induced by McC is mediated by (p)ppGpp and requires chromosomally encoded toxin‐antitoxin modules. McC‐producing cells have increased persistence levels due to a combined effect of McC imported from the cultured medium and intracellularly synthesized antibiotic. McC‐producing cells also induce persistence in sensitive cells during co‐cultivation, underscoring complex interactions in bacterial communities where an antagonistic compound produced by one community member can benefit other members by increasing their ability to withstand antibiotics.
Importance of the E. coli DinJ antitoxin carboxy terminus for toxin suppression and regulated proteolysis

Toxin–antitoxin genes play important roles in the regulation of bacterial growth during stress. One response to stress is selective proteolysis of antitoxin proteins which releases their cognate toxin partners causing rapid inhibition of growth. The features of toxin–antitoxin complexes that are important to inhibit toxin activity as well as to release the active toxin remain elusive. Furthermore, it is unclear how antitoxins are selected for proteolysis by cellular proteases. Here, we test the minimal structural requirements of the Escherichia coli DinJ antitoxin to suppress its toxin partner, YafQ. We find that DinJ–YafQ complex formation is critically dependent on the last ten C‐terminal residues of DinJ. However, deletion of these 10 DinJ residues has little effect on transcriptional autorepression suggesting that the YafQ toxin is not a critical component of the repression complex in contrast to other toxin–antitoxin systems. We further demonstrate that loop 5 preceding these ten C‐terminal residues is important for Lon‐mediated proteolysis. These results provide important insights into the critical interactions between toxin–antitoxin pairs necessary to inhibit toxin activity and the regulated proteolysis of antitoxins.
Prevalence Of Sun Protection, Skin Self-Examination And Skin Cancer Screening Behaviours And Practices Among Medical Students in Tirana, Albania With Family History For Skin Cancer

Introduction Cutaneous malignant melanoma prevalence, incidence and mortality rates are increasing in white populations worldwide more rapidly than any other cancer site (American Cancer Society, 2006). Despite the potential importance of regular skin self­examination and promotion of self­protection practices, little is known about the prevalence of these practices in medical students in Albanian population. Methods This is a descriptive, quantitative cross­sectional study. In this study were included a sample of 150 individuals chosen among the students of Faculty of Medicine based on their family history for skin cancer. This study was started on October the 3rd and finished on November the 12th. Subjects had to fill in a structured, self­administered questionnaire. All participants lived within Republic of Albania but at the time of the study were students in University of Tirana, Faculty of Medicine. Results In this study that we conducted we included 150 individuals supposed to have a risk for skin cancer based on their family history. 200 individuals were approached for participation. Of these, 150 individuals returned questionnaire data, yielding a response rate of 75% among eligible, successfully contacted participants. The mean age of the sample was 20.05 years (Std. Dev. = 0.925), with males (22%) and females (78%) represented unequally, because the gender configuration of the faculty itself has gender disparities with more than 80% females and only 20% male students. The majority of the sample was born in city or town (85.3%), 14.7% was born in a village. In terms of income level, 79.3% of participants had a medium income family background, 15.3% high income and 5.3% had a low income level family background. Conclusion It is important for those individuals with family history for skin cancer (which inherently indicates risk for skin cancer) to develop self­examination and SSE behaviours and practices in order to have a protection and at least an early detection (if onset) of the different forms of Melanoma. The results of this study provide some guide as to the key areas or 'hot spots' on which to focus attention when designing supportive care interventions for melanoma survivors and those at high risk of skin cancer.
Fibrinogen as a risk factor for coronary heart disease and mortality in middle-aged men and women. The Scottish Heart Health Study.

AIMS Fibrinogen was measured in 5095 men and 4860 men aged 40-59 in a random population sample from 25 districts of Scotland recruited during 1984-87: the Scottish Heart Health Study. Fibrinogen was then related to the chance of fatal and non-fatal coronary events and death from any cause during a subsequent follow-up period of around 8 years. METHODS AND RESULTS Fibrinogen was measured by the Clauss assay. The effect of fibrinogen on coronary heart disease and death was assessed through age-adjusted means and Cox proportional hazards regression models, accounting for age, cotinine (a measure of tobacco smoke inhalation) and 11 other major coronary risk factors. Fibrinogen was found to be an important risk factor for coronary heart disease in men and women, with and without pre-existing coronary heart disease. There appears to be a threshold effect, with those in the highest fifth of the distribution having a much increased risk. Estimated age-adjusted hazard ratios by sex and pre-existing coronary heart disease group for the highest to lowest fifth of fibrinogen range between 1.93 and 4.86. Fibrinogen is also important as a risk factor for coronary death and all-causes mortality, with a similar threshold effect. Comparing the two extreme fifths, the hazard ratios for coronary death are 3.01 and 3.42, and for all-cause mortality are 2.59 and 2.20, for men and women respectively. Adjustment for cotinine reduces the hazard ratios, but further adjustment for the other 11 risk factors has little effect for coronary heart disease events. After full adjustment there is a remaining significant (P < 0.05) hazard ratio for coronary death and death from any cause and for a coronary heart disease event for those free of coronary heart disease at baseline, amongst men, comparing the highest to the lowest fifth. CONCLUSION Fibrinogen is a strong predictor of coronary heart disease, fatal or non-fatal, new or recurrent, and of death from an unspecified cause, for both men and women. Its effect is only partially attributable to other coronary risk factors, the most important of which is smoking.
The inactivation of rfaP, rarA or sspA gene improves the viability of the Escherichia coli DNA polymerase III holD mutant

The Escherichia coli holD mutant is poorly viable because the stability of holoenzyme polymerase III (Pol III HE) on DNA is compromised. Consequently, the SOS response is induced and the SOS polymerases DinB and Pol II further hinder replication. Mutations that restore the holD mutant viability belong to two classes, those that stabilize Pol III on DNA and those that prevent the deleterious effects of DinB over‐production. We identified a dnaX mutation and the inactivation of rfaP and sspA genes as belonging to the first class of holD mutant suppressors. dnaX encodes a Pol III clamp loader subunit that interacts with HolD. rfaP encodes a lipopolysaccharide kinase that acts in outer membrane biogenesis. Its inactivation improves the holD mutant growth in part by affecting potassium import, previously proposed to stabilize Pol III HE on DNA by increasing electrostatic interactions. sspA encodes a global transcriptional regulator and growth of the holD mutant in its absence suggests that SspA controls genes that affect protein‐DNA interactions. The inactivation of rarA belongs to the second class of suppressor mutations. rarA inactivation has a weak effect but is additive with other suppressor mutations. Our results suggest that RarA facilitates DinB binding to abandoned forks.
Silver potentiates aminoglycoside toxicity by enhancing their uptake

The predicted shortage in new antibiotics has prompted research for chemicals that could act as adjuvant and enhance efficacy of available antibiotics. In this study, we tested the effects of combining metals with aminoglycosides on Escherichia coli survival. The best synergizing combination resulted from mixing aminoglycosides with silver. Using genetic and aminoglycoside uptake assays, we showed that silver potentiates aminoglycoside action in by‐passing the PMF‐dependent step, but depended upon protein translation. We showed that oxidative stress or Fe–S cluster destabilization were not mandatory factors for silver potentiating action. Last, we showed that silver allows aminoglycosides to kill an E. coli gentamicin resistant mutant as well as the highly recalcitrant anaerobic pathogen Clostridium difficile. Overall this study delineates the molecular basis of silver's potentiating action on aminoglycoside toxicity and shows that use of metals might offer solutions for battling against increased bacterial resistance to antibiotics.
The trans‐envelope architecture and function of the type 2 secretion system: new insights raising new questions

Nanomachines belonging to the type IV filament (Tff) superfamily serve a variety of cellular functions in prokaryotes, including motility, adhesion, electrical conductance, competence and secretion. The type 2 secretion system (T2SS) Tff member assembles a short filament called pseudopilus that promotes the secretion of folded proteins from the periplasm across the outer membrane of Gram‐negative bacteria. A combination of structural, biochemical, imaging, computational and in vivo approaches had led to a working model for the assembled nanomachine. High‐resolution cryo‐electron microscopy and tomography provided the first view of several homologous Tff nanomachines in the cell envelope and revealed the structure of the outer membrane secretin channel, challenging current models of the overall stoichiometry of the T2SS. In addition, recent insights into exoprotein substrate features and interactions with the T2SS have led to new questions about the dynamics of the system and the role of the plasma membrane in substrate presentation. This micro‐review will highlight recent advances in the field of type 2 secretion and discuss approaches that can be used to reach a mechanistic understanding of exoprotein recognition, integration into the machine and secretion.
Prevalence and genotypes of Campylobacter jejuni from urban environmental sources in comparison with clinical isolates from children.

This study aimed to investigate the prevalence of Campylobacter jejuni in potential contamination sources that are not regularly monitored such as free-living urban pigeons and crows, dogs, cats and urban environmental water and to assess the possible impact on the epidemiology of campylobacteriosis in children using multilocus sequence typing (MLST). Campylobacter spp. were detected in 36.2 % of faecal samples of free-living urban birds and in 40.4 % of environmental water samples. A low prevalence of Campylobacter spp. was detected in dogs and cats, with 7.9 and 9.1 %, respectively. Further identification of isolates revealed that environmental water and pet samples were mostly contaminated by other Campylobacter spp. than C. jejuni, whereas C. jejuni was the most prevalent species in faecal samples of free-living birds (35.4 %). This species was the dominant cause of campylobacteriosis in children (91.5 %). In addition, the diversity of C. jejuni MLST types in free-living birds and children was investigated. Clonal complex (CC) 179 was predominant among free-living urban birds; however, only two isolates from children were assigned to this CC. One dog and one child isolate were assigned to the same clonal complex (CC48) and sequence type (ST) 918. The dominant two clonal complexes among the child clinical isolates (CC353 and CC21) were not detected among C. jejuni strains isolated from environmental sources examined in this study. As only two CCs were shared by environmental and child C. jejuni isolates and a high number of novel alleles and STs were found in C. jejuni isolated from free-living urban birds and environmental water, there is probably only a limited link between urban environmental sources and campylobacteriosis in children, particularly in rather cold climatic conditions.
p16(INK4a) expression begins early in human colon neoplasia and correlates inversely with markers of cell proliferation.

BACKGROUND & AIMS p16(INK4a) is a cell cycle inhibitor and a major tumor-suppressor protein, but the regulation of p16(INK4a) is poorly understood and the physiologic settings in which it exerts its antiproliferative effects are unknown. A role for p16(INK4a) in intestinal neoplasia is suggested by the observation that the promoter region is methylated in a subset of human colon tumors. We examined the expression of the protein in specimens representing the full spectrum of neoplastic progression in the human colon and determined whether expressing cells showed evidence of cell cycle inhibition. METHODS We studied p16(INK4a) expression by immunoprecipitation, immunoblotting, reverse-transcription polymerase chain reaction (RT-PCR), immunohistochemistry, and immunofluorescence in matched normal and neoplastic colonic tissue from 70 patients. RESULTS p16(INK4a) expression was very low in normal mucosa, with staining observed in rare epithelial cells at the base of crypts. A distinctly higher expression was found in 4 of 7 aberrant crypt foci, 32 of 36 adenomas, 18 of 28 primary carcinomas, and 5 of 5 metastatic carcinomas. Within each neoplasm p16(INK4a) staining was heterogeneous, with higher expression commonly seen in areas bordering normal tissue. p16(INK4a) staining correlated inversely with that of Ki67, cyclin A, and the retinoblastoma protein, suggesting that cell cycle progression was inhibited. CONCLUSIONS These results suggest that p16(INK4a) expression begins in the earliest detectable stages of neoplastic progression in the human colon and exerts a continuous, piecemeal constraint on tumor growth.
Functional assignment of multiple ESCRT‐III homologs in cell division and budding in Sulfolobus islandicus

The archaea Sulfolobus utilizes the ESCRT‐III‐based machinery for cell division. This machinery comprises three proteins: CdvA, Eukaryotic‐like ESCRT‐III and Vps4. In addition to ESCRT‐III, Sulfolobus cells also encode three other ESCRT‐III homologs termed ESCRT‐III‐1, −2 and −3. Herein, we show that ESCRT‐III‐1 and −2 in S. islandicus REY15A are localized at midcell between segregating chromosomes, indicating that both are involved in cell division. Genetic analysis reveals that escrt‐III‐2 is indispensable for cell viability and cells with reduced overall level of ESCRT‐III‐1 exhibit growth retardation and cytokinesis defect with chain‐like cell morphology. In contrast, escrt‐III‐3 is dispensable for cell division. We show that S. islandicus REY15A cells generate buds when infected with S. tengchongensis spindle shaped‐virus 2 (STSV2) or when ESCRT‐III‐3 is over‐expressed. Interestingly, Δescrt‐III‐3 cells infected with STSV2 do not produce buds. These results suggest that ESCRT‐III‐3 plays an important role in budding. In addition, cells over‐expressing the C‐terminal truncated mutants of ESCRT‐III, ESCRT‐III‐1 and ESCRT‐III‐2 are maintained predominantly at the early, late, and membrane abscission stages of cell division respectively, suggesting a crucial role of the ESCRTs at different stages of membrane ingression. Intriguingly, intercellular bridge and midbody‐like structures are observed in cells over‐expressing MIM2‐truncated mutant of ESCRT‐III‐2.
Identification and characterization of a novel gastric peptide hormone: the motilin-related peptide.

BACKGROUND & AIMS This study looked for new proteins with expression restricted to the gastric epithelium that may provide insight to the differentiation and function of the gastric unit. METHODS A novel complementary DNA was isolated and sequenced, and its expression was examined in mouse tissues at both messenger RNA and protein levels. Subcellular localization was studied using immunoelectron microscopy. The posttraductional processing of the protein was analyzed in vitro by protein microsequencing and in vivo by Western blotting. RESULTS We identified a novel protein that is mainly expressed by the secretory granules of the stomach enteroendocrine cells. This protein has sequence similarity with prepromotilin, the precursor of the motilin hormone and the motilin-associated peptide. As for the prepromotilin, a posttraductional maturation leads to a secreted peptide that is further cleaved at a dibasic site and gives rise to the motilin-related peptide (MTLRP) and MTLRP-associated peptide. CONCLUSIONS We have identified and characterized a novel gene encoding the preproMTLRP protein. MTLRP presents similarity to motilin and is specifically expressed by enteroendocrine cells of the stomach and therefore represents a novel hormone.
Cell wall peptidolipids of Mycobacterium avium: from genetic prediction to exact structure of a nonribosomal peptide

Mycobacteria have a complex cell wall structure that includes many lipids; however, even within a single subspecies of Mycobacterium avium these lipids can differ. Total lipids from an M. avium subsp. paratuberculosis (Map) ovine strain (S‐type) contained no identifiable glycopeptidolipids or lipopentapeptide (L5P), yet both lipids are present in other M. avium subspecies. We determined the genetic and phenotypic basis for this difference using sequence analysis as well as biochemical and physico‐chemical approaches. This strategy showed that a nonribosomal peptide synthase, encoded by mps1, contains three amino acid specifying modules in ovine strains, compared to five modules in bovine strains (C‐type). Sequence analysis predicted these modules would produce the tripeptide Phe‐N‐Methyl‐Val‐Ala with a lipid moiety, termed lipotripeptide (L3P). Comprehensive physico‐chemical analysis of Map S397 extracts confirmed the structural formula of the native L3P as D‐Phe‐N‐Methyl‐L‐Val‐L‐Ala‐OMe attached in N‐ter to a 20‐carbon fatty acid chain. These data demonstrate that S‐type strains, which are more adapted in sheep, produce a unique lipid. There is a dose‐dependent effect observed for L3P on upregulation of CD25+ CD8 T cells from infected cows, while L5P effects were static. In contrast, L5P demonstrated a significantly stronger induction of CD25+ B cells from infected animals compared to L3P.
Intestinal iron uptake determined by divalent metal transporter is enhanced in HFE-deficient mice with hemochromatosis.

BACKGROUND & AIMS Overexpression of duodenal divalent metal transporter (DMT1) messenger RNA occurs in hemochromatosis and HFE-knockout mice, suggesting that DMT1 mediates enhanced absorption of iron; however, increased expression of functional DMT1 protein has yet to be substantiated. We examined the role of DMT1 and the mucosal iron uptake defect in HFE-knockout mice. METHODS Unidirectional iron uptake of 59Fe by small intestinal mucosa in vitro was compared between matched pairs of HFE-knockout and wild-type mice. DMT1-specific antibodies were used to block iron transport and to quantify duodenal protein expression. RESULTS Ferrous iron uptake at 3.5-450 micromol/L was greatly enhanced in HFE-knockouts compared with wild-type, the apparent V(max) for Fe2+ transport being doubled (P < 0.01). Supplied as Fe3+, uptake was only enhanced in HFE-knockouts at < or =18 micromol/L, when the iron was almost completely converted to Fe2+ by mucosal ferrireductases. DMT1 antibody reduced the apparent Vmax for mucosal Fe2+ transport in HFE-knockouts to below wild-type control values (P < 0.02); immunoreactive mucosal DMT1 protein was increased nearly 2-fold in HFE-knockouts (P < 0.01). CONCLUSIONS Disruption of the HFE gene up-regulates functional DMT1 transporters and enhances uptake of ferrous iron by this mechanism; DMT1 also mediates increased uptake after reduction of ferric iron presented at physiological concentrations.
Effects of ursodeoxycholic and cholic acid feeding on hepatocellular transporter expression in mouse liver.

BACKGROUND AND AIMS Cholestasis is associated with retention of potentially toxic bile acids and alterations in hepatocellular transporter expression. Conversely, nontoxic ursodeoxycholic acid (UDCA) stimulates bile secretion and counteracts cholestasis. This study aimed to determine the effects of UDCA and cholic acid (CA) on the expression of hepatocellular transporters for bile acids (Ntcp, Bsep), organic anions (Oatp1, Mrp2), organic cations (Mdr1a/b), and phospholipids (Mdr2) in mouse liver. METHODS Bile flow/composition was analyzed in UDCA- or CA-fed mice. Transporter expression was studied by reverse-transcription polymerase chain reaction, Western blotting, and immunofluorescence microscopy. RESULTS UDCA had no effect on basolateral Ntcp and down-regulated Oatp1, whereas canalicular Bsep and Mrp2 were up-regulated. CA down-regulated basolateral Ntcp and Oatp1, whereas canalicular Bsep, Mrp2, and Mdr1a/b were up-regulated. Neither UDCA nor CA affected Mdr2 expression. Both UDCA and CA stimulated biliary bile acid and glutathione excretion, although only CA increased phospholipid and cholesterol excretion. CONCLUSIONS Down-regulation of basolateral and up-regulation of canalicular transporters in response to CA may represent a defense mechanism, in an attempt to prevent hepatocellular accumulation of potentially toxic bile acids. The therapeutic effects of UDCA may be caused in part by stimulation of canalicular transporter expression in the absence of hepatocellular toxicity.
Anti-tissue transglutaminase antibodies and EEG pattern in celiac patients on prolonged gluten-free diet

The Authors investigate the relationship between serum anti-tTG antibodies and EEG pattern in 12 celiac patients of various age on gluten-free diet for 1-10 years. In a group of 6 patients with good compliance with the diet, anti-tTG antibodies were normal in all and EEG in 5; in another group of 6 patients with poor compliance with the diet, serum anti-tTG antibodies were raised in all; EEG abnormalities of various gravity were reported in 5 patients. The concomitance of raised anti-tTG antibodies and EEG abnormalities is stressed, as possible expression of an immune-inflammatory reaction persistent in Central Nervous System.
AGA technical review on osteoporosis in gastrointestinal diseases.

Abstract Osteoporosis is increasingly recognized as a source of significant disability, an awareness that has prompted clinicians to actively pursue the diagnosis among high-risk patients. Fractures have an obvious associated morbidity, negative impact on quality of life, and both direct and indirect costs. Hip fractures have long been associated with an increased mortality rate, but only recently has excessive mortality also been shown to accompany non–hip fractures and low bone mass. 1-3 The excessive mortality associated with fractures is largely confined to elderly males and postmenopausal females. Many patients with gastrointestinal (GI) disorders at risk for osteoporosis are young, and these data may not apply to them. Much of the available clinical information regarding osteoporosis screening, outcomes, and therapeutic interventions is derived from the postmenopausal osteoporosis literature. It is recognized, however, that osteoporosis may accompany many other medical conditions, occurring as a sequela to disease or even to its treatment. GASTROENTEROLOGY 2003;124:795-841