Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins”

The Escherichia coli mazEF module is one of the most thoroughly studied toxin–antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. MazF is an endoribonuclease that leads to the inhibition of protein synthesis by cleaving mRNAs at ACA sequences. Here, using 2D-gels, we show that in E. coli, although MazF induction leads to the inhibition of the synthesis of most proteins, the synthesis of an exclusive group of proteins, mostly smaller than about 20 kDa, is still permitted. We identified some of those small proteins by mass spectrometry. By deleting the genes encoding those proteins from the E. coli chromosome, we showed that they were required for the death of most of the cellular population. Under the same experimental conditions, which induce mazEF-mediated cell death, other such proteins were found to be required for the survival of a small sub-population of cells. Thus, MazF appears to be a regulator that induces downstream pathways leading to death of most of the population and the continued survival of a small sub-population, which will likely become the nucleus of a new population when growth conditions become less stressful

A Conditional Yeast E1 Mutant Blocks the Ubiquitin–Proteasome Pathway and Reveals a Role for Ubiquitin Conjugates in Targeting Rad23 to the Proteasome

E1 ubiquitin activating enzyme catalyzes the initial step in all ubiquitin-dependent processes. We report the isolation of uba1-204, a temperature-sensitive allele of the essential Saccharomyces cerevisiae E1 gene, UBA1. Uba1-204 cells exhibit dramatic inhibition of the ubiquitin–proteasome system, resulting in rapid depletion of cellular ubiquitin conjugates and stabilization of multiple substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play in the dynamic interaction of the UbL/UBA adaptor proteins Rad23 and Dsk2 with the proteasome. Although proteasomes purified from mutant cells are intact and proteolytically active, they are depleted of ubiquitin conjugates, Rad23, and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo

A linguistic analysis of lying in negative evaluations: The speech act performance of Chinese learners of Korean

이 논문은 중국인 한국어 학습자와 한국어 화자들 사이의 ‘거짓말’ 화행 양상을 언어학적으로 분석한 연구이다. 여기서 말하는 ‘거짓말’이란 요청, 사과, 거절 등과 같은 화행의 일종으로서 ‘부정적 평가’에 속하며 대화 참여자나 상황을 고려한 소위 ‘선의의 거짓말’을 가리키는 것으로 이해할 수 있을 것이다. 우리는 중국인 한국어 학습자 15명과 한국어 화자 15명을 대상으로 담화완성테스트(DCT)와 부연설명질문지(QFE)를 사용하여 피실험자들의 화행을 분석하였다. 피실험자 자신들의 설명과 한국어교육 전문가 다섯 명의 판정을 종합해 ‘거짓말’ 화행을 가려내고 통계 처리를 바탕으로 다음과 같은 결론에 도달했다. 한국어 화자들이 중국인 한국어 학습자들보다 (선의의) 거짓말을 더 많이 수행하는 것으로 나타났다. 그리고 두 집단 모두 부정적 평가가 사물에 관련된 경우보다 사람에 관련된 경우에 ‘거짓말’ 화행을 더 많이 사용한다. 그러나 화자와 청자 사이의 친소관계(distance)나 상하관계(power)는 거짓말 사용에 직접적 상관 관계를 보여주지 않았다. 이 연구는 지금까지 화행 연구 중에서 상대적으로 연구가 부진했던 부정평가와 ‘거짓말’ 화행에 대한 분석을 시도했다는 점에서 의미가 있다. 또한 한국어 화자와 중국인 한국어 학습자 사이에 보이는 화행 수행의 차이를 문화인식(cultural awareness)의 관점에서 해석해 볼 수 있는 가능성도 열어 주었다

Nottingham prognostic index plus (NPI+) predicts risk of distant metastases in primary breast cancer

The Nottingham prognostic index plus (NPI+) is based on the assessment of biological class combined with established clinicopathologic prognostic variables providing improved patient outcome stratification for breast cancer superior to the traditional NPI. This study aimed to determine prognostic capability of the NPI+ in predicting risk of development of distant disease. A well-characterised series of 1073 primary early-stage BC cases treated in Nottingham and 251 cases from Budapest were immunohistochemically assessed for cytokeratin (Ck)5/6, Ck18, EGFR, oestrogen receptor (ER), progesterone receptor, HER2, HER3, HER4, Mucin 1 and p53 expression. NPI+ biological class and prognostic scores were assigned using individual algorithms for each biological class incorporating clinicopathologic parameters and investigated in terms of prediction of distant metastases-free survival (MFS). The NPI+ identified distinct prognostic groups (PG) within each molecular class which were predictive of MFS providing improved patient outcome stratification superior to the traditional NPI. NPI+ PGs, between series, were comparable in predicting patient outcome between series in luminal A, basal p53 altered and HER2+/ER+ (p > 0.01) tumours. The low-risk groups were similarly validated in luminal B, luminal N, basal p53 normal tumours (p > 0.01). Due to small patient numbers the remaining PGs could not be validated. NPI+ was additionally able to predict a higher risk of metastases at certain distant sites. This study may indicate the NPI+ as a useful tool in predicting the risk of metastases. The NPI+ provides accurate risk stratification allowing improved individualised clinical decision making for breast cancer

Pathological non-response to chemotherapy in a neoadjuvant setting of breast cancer: an inter-institutional study

To identify markers of non-response to neoadjuvant chemotherapy (NAC) that could be used in the adjuvant setting. Sixteen pathologists of the European Working Group for Breast Screening Pathology reviewed the core biopsies of breast cancers treated with NAC and recorded the clinico-pathological findings (histological type and grade; estrogen, progesterone receptors, and HER2 status; Ki67; mitotic count; tumor-infiltrating lymphocytes; necrosis) and data regarding the pathological response in corresponding surgical resection specimens. Analyses were carried out in a cohort of 490 cases by comparing the groups of patients showing pathological complete response (pCR) and partial response (pPR) with the group of non-responders (pathological non-response: pNR). Among other parameters, the lobular histotype and the absence of inflammation were significantly more common in pNR (p < 0.001). By ROC curve analyses, cut-off values of 9 mitosis/2 mm(2) and 18 % of Ki67-positive cells best discriminated the pNR and pCR + pPR categories (p = 0.018 and < 0.001, respectively). By multivariable analysis, only the cut-off value of 9 mitosis discriminated the different response categories (p = 0.036) in the entire cohort. In the Luminal B/HER2- subgroup, a mitotic count < 9, although not statistically significant, showed an OR of 2.7 of pNR. A lobular histotype and the absence of inflammation were independent predictors of pNR (p = 0.024 and < 0.001, respectively). Classical morphological parameters, such as lobular histotype and inflammation, confirmed their predictive value in response to NAC, particularly in the Luminal B/HER2- subgroup, which is a challenging breast cancer subtype from a therapeutic point of view. Mitotic count could represent an additional marker but has a poor positive predictive value

Prognostic impact of macrometastasis linear size in sentinel node biopsy for breast carcinoma

AIM: The aim of the present study was to evaluate the risk of axillary non-sentinel lymph-node metastases (ALN) in breast cancer patients presenting macrometastasis (Mac-m) in the sentinel lymph node (SN). MATERIALS AND METHODS: A retrospective series of 1464 breast cancers from patients who underwent ALN dissection following the diagnosis of Mac-m in the sentinel node (SN) was studied. In all the cases the MAC-m linear size was evaluated and correlated with presence or absence of non-SN ALN metastases. RESULTS: Non-SN metastases were detected in 644\1464 cases (43.98%). The risk of further axillary metastases ranged from 20.2% (37/183) in cases with Mac-m between 2 and 2.9 mm, to 65.3% (262/401) in cases with Mac-m measuring > 10 mm. The risk of non-SN ALN metastases showed a 3% increase, parallel to each mm increment in SN metastasis size. The data evaluated with the receiver operating characteristic (ROC) curve showed that the Mac-m could be subdivided according to a new cut-off of 7 mm. pT1 tumours, with Mac-m < 7 mm had a risk of non-SN ALN metastases of <30%. Furthermore 109/127 of these (85.8%) had 3 or less non-SN ALN -metastases. CONCLUSIONS: The present data give a detailed description on the risk of non-SN ALN involvement, that may be useful in the evaluation of breast cancer patients. It is suggested that a Mac-m size of <7 mm is related to a low residual axillary disease burden in breast cancer patients with small (pT1) tumours

Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and has become a global health threat. No HCV vaccine is currently available and treatment with antiviral therapy is associated with adverse side effects. Moreover, there is no preventive therapy for recurrent hepatitis C post liver transplantation. The NS3 serine protease is necessary for HCV replication and represents a prime target for developing anti HCV therapies. Recently we described a therapeutic approach for eradication of HCV infected cells that is based on protein delivery of two NS3 protease-activatable recombinant toxins we named “zymoxins”. These toxins were inactivated by fusion to rationally designed inhibitory peptides via NS3-cleavable linkers. Once delivered to cells where NS3 protease is present, the inhibitory peptide is removed resulting in re-activation of cytotoxic activity. The zymoxins we described suffered from two limitations: they required high levels of protease for activation and had basal activities in the un-activated form that resulted in a narrow potential therapeutic window. Here, we present a solution that overcame the major limitations of the “first generation zymoxins” by converting MazF ribonuclease, the toxic component of the E. coli chromosomal MazEF toxin-antitoxin system, into an NS3-activated zymoxin that is introduced to cells by means of gene delivery. We constructed an expression cassette that encodes for a single polypeptide that incorporates both the toxin and a fragment of its potent natural antidote, MazE, linked via an NS3-cleavable linker. While covalently paired to its inhibitor, the ribonuclease is well tolerated when expressed in naïve, healthy cells. In contrast, activating proteolysis that is induced by even low levels of NS3, results in an eradication of NS3 expressing model cells and HCV infected cells. Zymoxins may thus become a valuable tool in eradicating cells infected by intracellular pathogens that express intracellular proteases

ONEST (Observers Needed to Evaluate Subjective Tests) Analysis of Stromal Tumour-Infiltrating Lymphocytes (sTILs) in Breast Cancer and Its Limitations

Simple Summary Tumour-infiltrating lymphocytes (TILs) reflect the host's response against tumours. TILs have a strong prognostic effect in the so-called triple-negative (oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2 negative) subset of breast cancers and predict a better response when primary systemic (neoadjuvant) treatment is administered. Although they are easy to assess, their quantitative assessment is subject to some inter-observer variation. ONEST (Observers Needed to Evaluate Subjective Tests) is a new way of analysing inter-observer variability and helps in estimating the number of observers required for a more reliable estimation of this phenomenon. This aspect of reproducibility for TILs has not been explored previously. Our analysis suggests that between six and nine pathologists can give a good approximation of inter-observer agreement in TIL assessments. Tumour-infiltrating lymphocytes (TILs) reflect antitumour immunity. Their evaluation of histopathology specimens is influenced by several factors and is subject to issues of reproducibility. ONEST (Observers Needed to Evaluate Subjective Tests) helps in determining the number of observers that would be sufficient for the reliable estimation of inter-observer agreement of TIL categorisation. This has not been explored previously in relation to TILs. ONEST analyses, using an open-source software developed by the first author, were performed on TIL quantification in breast cancers taken from two previous studies. These were one reproducibility study involving 49 breast cancers, 23 in the first circulation and 14 pathologists in the second circulation, and one study involving 100 cases and 9 pathologists. In addition to the estimates of the number of observers required, other factors influencing the results of ONEST were examined. The analyses reveal that between six and nine observers (range 2-11) are most commonly needed to give a robust estimate of reproducibility. In addition, the number and experience of observers, the distribution of values around or away from the extremes, and outliers in the classification also influence the results. Due to the simplicity and the potentially relevant information it may give, we propose ONEST to be a part of new reproducibility analyses

Shifting Characterizations of the ‘Common People’ in Modern English Retranslations of Thucydides’ History of the Peloponnesian War: A corpus-based analysis

Little research has yet explored the impact of (re)translation on narrative characterization, that is, on the process through which the various actors depicted in a narrative are attributed particular traits and qualities. Moreover, the few studies that have been published on this topic are either rather more anecdotal than systematic, or their focus is primarily on the losses in character information that inevitably occur when a narrative is retold for a new audience in a new linguistic context. They do not explore how the translator’s own background knowledge and ideological beliefs might affect the characterization process for readers of their target-language text. Consequently, this paper seeks to make two contributions to the field: first, it presents a corpus-based methodology developed as part of the Genealogies of Knowledge project for the comparative analysis of characterization patterns in multiple retranslations of a single source text. Such an approach is valuable, it is argued, because it can enhance our ability to engage in a more systematic manner with the accumulation of characterization cues spread throughout a narrative. Second, the paper seeks to move discussions of the effects of translation on narrative characterization away from a paradigm of loss, deficiency and failure, promoting instead a perspective which embraces the productive role translators often play in reconfiguring the countless narratives through which we come to know, imagine and make sense of the past, our present and futures. The potential of this methodology and theoretical standpoint is illustrated through a case study exploring changes in the characterization of ‘the common people’ in two English-language versions of classical Greek historian Thucydides’ History of the Peloponnesian War, the first produced by Samuel Bloomfield in 1829 and the second by Steven Lattimore in 1998. Particular attention is paid to the referring expressions used by each translator—such as the multitude vs. the common people—as well as the specific attributes assigned to this narrative actor. In this way, the study attempts to gain deeper insight into the ways in which these translations reflect important shifts in attitudes within key political debates concerning the benefits and dangers of democracy