Two-dimensional gel electrophoresis in bacterial proteomics

Two-dimensional gel electrophoresis(2-DE)is a gel-based technique widely used for analyzing the pro-tein composition of biological samples.It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal bio-physical separation techniques:isoelectric focusing(first dimension)and polyacrylamide gel electrophore-sis(second dimension).2-DE is ideally suited for ana-lyzing the entire expressed protein complement of a bacterial cell:its proteome.Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of envi-ronmental and medically-relevant bacteria.Here we give a broad overview of the basic principles and his-torical development of gel-based proteomics,and how this powerful approach can be applied for studying bacterial biology and physiology.We highlight specific 2-DE applications that can be used to analyze when,where and how much proteins are expressed.The links between proteomics,genomics and mass spectrometry are discussed.We explore how proteomics involving tandem mass spectrometry can be used to analyze(post-translational)protein modifications or to identify proteins of unknown origin by de novo peptide se-quencing.The use of proteome fractionation tech-niques and non-gel-based proteomic approaches are also discussed.We highlight how the analysis of pro-teins secreted by bacterial cells(secretomes or exo-proteomes)can be used to study infection processes or the immune response.This review is aimed at non-specialists who wish to gain a concise,compre-hensive and contemporary overview of the nature and applications of bacterial proteomics.

A six-year descriptive epidemiological study of human coronavirus infections in hospitalized patients in Hong Kong

We conducted a six-year epidemiological study on human coronaviruses（HCoVs） circulating in Hong Kong, using 8275 nasopharyngeal samples from patients with acute respiratory tract infections. HCoVs were detected in 77（0.93%） of the samples by a pan-HCoV RT-PCR assay. The most frequently detected HCoV species was HCoV-OC43（0.58%）, followed by HCoV-229E（0.15%）,HCoV-HKU1（0.13%） and HCoV-NL63（0.07%）. HCoVs were detected throughout the study period（September 2008–August 2014）, with the highest detection rate from September 2010 to August2011（22/1500, 1.47%）. Different seasonal patterns of each HCoV species in Hong Kong were noted.HCoV-OC43 was predominant in the fall and winter, whereas HCoV-HKU1 showed peak activity in winter, with a few cases occurred in spring and summer. HCoV-229 E mainly occurred in winter and spring, while HCoV-NL63 was predominant in summer and autumn. HCoVs most commonly infect the elderly and young children, with median age of 79.5 years（range, 22 days to 95 years）.Intriguingly, the detection rate of HCoV-OC43 in the age group of ＆gt; 80 years（26/2380, 1.09%） was significantly higher than that in the age group of 0–10 years（12/2529, 0.47%）（P 〈 0.05）. These data provides new insight into the epidemiology of coronaviruses.

Severe Sepsis Caused by Listeria monocytogenes in A Patient Given Monoclonal Antibodies Against CD38 and Proteosome Inhibitor

Introduction Target therapies are widely used for treatment of various kinds of hematological malignancies.Since the cancer cells that are targeted,share the same markers with the non-cancerous cells of the immunological system,these therapies are often associated with infectious diseases that require the particular type of immune response for control.In this article,we report a case of Listeria monocytogenes bacteraemia complicating carfilzomib and daratumumab treatment for multiple myeloma.To the best of our knowledge,this is the first case report of listeriosis as a complication of monoclonal antibodies against CD38 and/or proteosome inhibitor therapy.

Romance of the three domains:how cladistics transformed the classifi cation of cellular organisms

Cladistics is a biological philosophy that uses genealogi-cal relationship among species and an inferred sequence of divergence as the basis of classifi cation.This review critically surveys the chronological development of bio-logical classification from Aristotle through our post-genomic era with a central focus on cladistics.In 1957,Julian Huxley coined cladogenesis to denote splitting from subspeciation.In 1960,the English translation of Willi Hennig’s 1950 work,Systematic Phylogenetics,was published,which received strong opposition from phenet-icists,such as numerical taxonomists Peter Sneath and Robert Sokal,and evolutionary taxonomist,Ernst Mayr,and sparked acrimonious debates in 1960-1980.In 1977-1990,Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellu-lar life and established major prokaryotic phyla.Cladistics has since dominated taxonomy.Despite being compatible with modern microbiological observations,i.e.organisms with unusual phenotypes,restricted expression of charac-teristics and occasionally being uncultivable,increasing recognition of pervasiveness and abundance of horizon-tal gene transfer has challenged relevance and validity of cladistics.The mosaic nature of eukaryotic and prokary-otic genomes was also gradually discovered.In the mid-2000s,high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life.While genomics only indirectly leads to understanding of func-tional adaptations to ecological niches,computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged.Controversies are not expected to settle as taxonomic classifi cations shall remain subjective to serve the human scientist,not the classifi ed.

Next-Generation Sequencing-Based Diagnosis of Bacteremic Listeria monocytogenes Meningitis in a Patient with Anti-Interferon Gamma Autoantibodies:A Case Report

Although various opportunistic infections have been described in patients with anti-interferon gamma autoantibodies,so far there is no Listeria monocytogenes infection reported to be associated with this primary immunodeficiency.Here,we describe the first case of bacteremic L.monocytogenes meningitis in a 59-year-old Chinese man with anti-interferon gamma autoantibodies,who presented with acute onset of fever and severe headache.Blood culture was positive but culture of the cerebrospinal fluid was negative,although it showed features suggestive of partially treated bacterial meningitis.The presence of L.monocytogenes in the cerebrospinal fluid was confirmed by next-generation sequencing.Avoidance of high-risk food items in these patients is important for the prevention of listeriosis.The use of antibiotic regimens that cover Listeria is crucial for empirical treatment,particularly if such patients develop acute or subacute meningitis.Next-generation sequencing is becoming an important diagnostic modality for culture-negative infections.

Sex Bias in Sample Collections From Bats,the Culprit of SARS Coronavirus,SARS-Coronavirus-2,and Other Emerging Viruses

Chiroptera is the second largest mammalian order in terms of species number.So far,there are more than 1400 known bat species across the six continents,making up 20%of the total number of mammalian species.1 Bats are well recognized to be the hosts of a number of highly pathogenic viruses,such as rabies virus,Hendra virus,Nipah virus,and Ebola virus,for a long time.2–5 Shortly after the severe acute respiratory syndrome(SARS)epidemic which originated from Southern China in 2003,we discovered that bats were the ultimate reservoir of SARSrelated coronavirus(SARSr-CoV).6 In 2012,the cause of the even more fatal Middle East respiratory syndrome(MERS)which originated from the Middle East was also found to be another CoV,MERS-CoV.7 The ancestor of MERS-CoV was also from bats.8,9 Recently,the COVID-19 outbreak that has already officially infected more than 13 million patients with more than 574000 deaths was also confirmed to be due to another betacoronavirus,named SARS coronavirus 2(SARS-CoV-2),from bats.10 Moreover,bat cell lines have also been harvested and propagated for the study of SARS-CoV,MERS-CoV,and SARS-CoV-2.

First Report of Tsukamurella conjunctivitidis CAPD-related Peritonitis

Introduction Using the information obtained from analysis of 16S rRNA gene sequences,Tsukamurella was first proposed as a genus in 1988,1 despite the fact that the first strain of this group of bacteria was described in 1941,2 and the first human isolate was reported in 1971.3 Similar to related genera of the order Corynebacteriales,such as Nocardia,Rhodococcus,and Gordonia,members of Tsukamurella are Gram-positive,aerobic,catalase-positive,and partially acid-fast as a result of the presence of mycolic acid in the cell envelope.Due to their similar phenotypic properties,differentiation of these genera and speciation within these genera is difficult in most clinical microbiology laboratories.

Streptococcus agalactiae Anterior Cervical Space and Superior Mediastinum Abscess in a Liver Transplant Recipient

Introduction Streptococcus agalactiae is most commonly associated with pregnancy-related infections,neonatal sepsis,and infections in patients with immunocompromised states,such as diabetes mellitus and malignancies.1 Although abscesses caused by S.agalactiae are sometimes encountered in immunocompromised patients,S.agalactiae abscess in transplant recipients is extremely rare.S.agalactiae abscesses have never been reported in liver transplant recipients.In this article,we report a case of S.agalactiae abscess in the anterior cervical space extending to the superior mediastinum in a liver transplant recipient.

Lemierre’s Syndrome Associated With Campylobacter rectus Bacteremia

Introduction Campylobacter rectus is a Gram-negative,anaerobic rod,first described in 1981 as Wolinella recta,subsequently re-classified to Campylobacter based on phylogenetic analysis in 1991.1 It is found in the oral cavity and gastrointestinal tract,and is mainly implicated in oral and periodontal infections.So far,there are only a handful of case reports in the literature describing extra-oral invasive C.rectus infections.2–6 Recently,we described a case of fatal C.rectus infection,due to subdural empyema and ruptured mycotic intracranial aneurysm.2 In this article,we report a case of Lemierre’s syndrome associated with C.rectus bacteremia.