Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

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Diversity in the immune system: “Preconceived ideas” or ideas preconceived?

Two concepts of the evolution and regulation of expression of the combining site repertoire of the immune system, are compared. One view is based on the Associative Recognition Theory as formulated by the author and the other is based on the Idiotype Network Idea as conceived by Jerne. The two concepts are analyzed from the point of view of their logic, internal consistency and factual support.     

Monitoring plant community change: an application of quadrat classification + discriminant analysis

A procedure for monitoring plant community change was described using data from 189 quadrats (each 0.09 m² in area) from or near 11 Carex exserta meadow sites in the high Sierra Nevada, California, USA. Initially the quadrats were agglomerated into five clusters by the flexible clustering strategy (beta=–0.25) with the standard absolute distance resemblance function. Data for each quadrat were cover percentages for C. exserta, other plants, litter, soil, gravel, and rock. The five clusters appeared to define a cover gradient, from quadrats with mostly gravel and rock to those with mostly C. exserta, and were accordingly designated pioneer, low seral, mid-seral, high seral, and climax.Classification functions (from discriminant analysis) are used with values of the variables to classify individual quadrats on sites used to monitor change. A site is characterized at repeated observations by the proportions of quadrats in each class. Within-class (low seral vs. low seral) rather than between-class (pioneer vs. low seral) tests are made for presence of change. Confidence intervals for differences in proportions of quadrats or individual quadrat probabilities of class membership are computed. If the confidence intervals do not cover zero, values for time one versus time two differ significantly.     

Detection of a protein encoded by a class II mitochondrial intron of Podospora anserina

Summary In the filamentous fungus Podospora anserina, the amplification as circular DNA molecules of the first intron (intron ) of the CO1 mitochondrial gene, encoding the cytochrome oxidase subunit 1, is known to be strongly associated with aging of strains. In this study we have attempted to detect the protein potentially encoded by the open reading frame (ORF) contained in this intron. This was done by the Western blot technique using specific antisera raised against three polypeptides encoded by three non-overlapping fragments of this ORF adapted to the universal code and overexpressed in Escherichia coli. We examined about thirty independent subclones of Podospora derived from two different geographic races (A, s), using wild-type and mutant strains, young and senescent cultures. A 100 kDa polypeptide, encoded by the class II intron , was detected in five senescent subclones which all showed strong amplification of the intronic sequence (Sen DNA ).     

Influences on the antimicrobial activity of surface-adsorbed nisin

The efficacy of the antimicrobial peptide nisin was examined after adsorption to silica surfaces. Three protocols were used to evaluate nisin's activity against adhered cells ofListeria monocytogenes: bioassay usingPediococcus pentosaceous FBB 61-2 as the sensitive indicator strain; visualization and enumeration of cells by microscopic image analysis; and viability of adhered cells as determined by lodonitrotetrazolium violet uptake and crystallization. The activity of adsorbed nisin was highly dependent upon conditions of adsorption. The highest antimicrobial activity of adsorbed nisin occurred with high concentrations of nisin (1.0 mg ml^–1) and brief contact times (1 h) on surfaces of low hydrophobicity. Sequential adsorption of a second protein (-lactoglobulin or bovine serum albumin) onto surfaces consistently resulted in decreased nisin activity. These data provide direction for the development of applications to limit microbial attachment on food contact surfaces through the use of adsorbed antimicrobial peptides.     

Sequence of the gene for a NAD(P)-dependent formaldehyde dehydrogenase (class III alcohol dehydrogenase) from a marine methanotroph Methylobacter marinus A45

Abstract A fragment of Methylobacter marinus A45 DNA has been cloned and sequenced, and an open reading frame has been identified that could code for a 46-kDa polypeptide. Comparison of the deduced amino acid sequence of the polypeptide against the protein data bank has revealed strong similarity with a number of alcohol dehydrogenases, with highest similarity towards class III alcohol dehydrogenases, which recently have been shown to be identical to glutathione-dependent formaldehyde dehydrogenases. We were unable to measure appreciable levels of NAD(P)-dependent formaldehyde dehydrogenases or alcohol dehydrogenase activities using aldehydes or primary or secondary alcohols in cell-free extracts from batch cultures of M. marinus A45. However, formaldehyde dehydrogenases activity was detected on zymograms. Our data suggest that, although NAD(P)-linked formaldehyde dehydrogenase or alcohol dehydrogenase activities are undetectable in cell-free extracts of most methylotrophs employing the ribulose monophosphate pathway for formaldehyde assimilation and dissimilation, the gene encoding formaldehyde dehydrogenase is present in M. marinus A45 and may be present in more of these organisms as well.     

正廿面体病毒的三角形剖分数和壳粒数公式的推导

本文对p=h~2+hk+k~2,T=pf~2,C=10T+2和C=10p(n-1)~2+2几个公式进行了新的推导和计算,并对其公式间的关系和每个参数的数学含义作了说明,进而澄清了一些模糊认识,加深了对公式的理解和运用。     

细菌素Paracin 1.7的纯化与性质

[目的]分离纯化(Lactobacillus paracasei)HD1.7所产生的细菌素并分析其特性.[方法]细菌素Paracin1.7的纯化采用色谱技术,其分子量检测采用十二烷基磺酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE),利用琼脂扩散法测定细菌素活力.[结果]Paracin 1.7分离于我国传统发酵食品酸菜发酵液中,其产生菌为副干酪乳杆菌.Paracin 1.7可以抑制其它微生物的生长,为细菌素.该菌在稳定期可产生大量Paracin 1.7.经过阳离子交换层析、凝胶过滤层析以及高效液相色谱(HPLC),对该细菌素进行了初步纯化,并经Tricine-SDS-PAGE检测其分子量大约为11 kDa.Paracin 1.7抑菌谱较广,其抑菌范围包括Proteus,Bacillus,Enterobacter,Staphylococcus,Escherichia,Lactobacillus,Microccus,Pseudomonas,Salmonella,Saccharomyces,其中有些为食品源致病菌.该细菌素在酸性及高温下稳定,对几种蛋白质酶敏感.该细菌素对敏感菌株的作用方式为抑菌.在4℃保存4个月后,Paraein 1.7的抑菌活性保持稳定.[结论]基于细菌素Paracin 1.7的性质,该细菌素可用作食品防腐剂.     

Inhibition of Listeria monocytogenes by freeze-dried piscicocin CS526 fermentate in food

AIMS: The effectiveness of freeze-dried powder, fermented with bacteriocin producing Carnobacterium piscicola CS526, was evaluated for the inhibition of Listeria monocytogenes in a food model. METHODS AND RESULTS: A 10% solution of milk whey powder was fermented with a bacteriocinogenic C. piscicola CS526 Bac(+) or its nonbacteriocinogenic mutant strain CS526 Bac(-) at 30 degrees C for 12 h and freeze-dried. The freeze-dried piscicocin CS526 Bac(+) fermentate exhibited strong anti-listerial activity even at a concentration of 1% (w/v) in sterile water (pH 7), but the piscicocin CS526 Bac(-) fermentate and nonfermented whey powder had no anti-listerial activity. In the presence of 10% piscicocin CS526 Bac(+) fermentate, L. monocytogenes in ground meat rapidly decreased from 10(5) CFU g(-1) to less than the detection limit (3.0 x 10(3) CFU g(-1)) within 5 and 1 days at 4 and 12 degrees C, and was bacteriostatically inhibited for 25 and 4 days at 4 and 12 degrees C respectively. Furthermore, this inhibitory effect was enhanced at lower temperatures. CONCLUSIONS: Piscicocin CS526 Bac(+) fermentate was effective for the control of L. monocytogenes in a food model at refrigeration temperatures. SIGNIFICANCE AND IMPACT OF THE STUDY: A freeze-dried bioactive piscicocin CS526 Bac(+) powder can be a powerful tool to ensure food safety against L. monocytogenes contamination in refrigerated foods such as ready-to-eat products.     

Identification and characterization of the retinoic acid response elements in the human RIG1 gene promoter

The expression of retinoic acid-induced gene 1 (RIG1), a class II tumor suppressor gene, is induced in cells treated with retinoids. RIG1 has been shown to express ubiquitously and the increased expression of this gene appears to suppress cell proliferation. Recent studies also demonstrated that this gene may play an important role in cell differentiation and the progression of cancer. In spite of the remarkable regulatory role of this protein, the molecular mechanism of RIG1 expression induced by retinoids remains to be clarified. The present study was designed to study the molecular mechanism underlying the all-trans retinoic acid (atRA)-mediated induction of RIG1 gene expression. Polymerase chain reaction was used to generate a total of 10 luciferase constructs that contain various fragments of the RIG1 5'-genomic region. These constructs were then transfected into human gastric cancer SC-M1 and breast cancer T47D cells for transactivation analysis. atRA exhibited a significant induction in luciferase activity only through the -4910/-5509 fragment of the 5'-genomic region of RIG1 gene relative to the translation initiation site. Further analysis of this promoter fragment indicated that the primary atRA response region is located in between -5048 and -5403 of the RIG1 gene. Within this region, a direct repeat sequence with five nucleotide spacing, 5'-TGACCTctattTGCCCT-3' (DR5, -5243/-5259), and an inverted repeat sequence with six nucleotide spacing, 5'-AGGCCAtggtaaTGGCCT-3' (IR6, -5323/-5340), were identified. Deletion and mutation of the DR5, but not the IR6 element, abolished the atRA-mediated activity. Electrophoretic mobility shift assays with nuclear extract from atRA-treated cells indicated the binding of retinoic acid receptor (RAR) and retinoid X receptor (RXR) heterodimers specifically to this response element. In addition to the functional DR5, the region contains many other potential sequence elements that are required to maximize the atRA-mediated induction. Taken together, we have identified and characterized the functional atRA response element that is responsible for the atRA-mediated induction of RIG1 gene.