bluuebunny/crossref_metadata_2025 huggingface dataset:
Sarcoptes scabiei: an important exotic pathogen of wombats
Authors: F Skerratt Lee
Published: April 2020

Sarcoptes scabiei is a parasitic astigmatid mite, which causes scabies in people and sarcoptic mange in mammals. Importantly, it is an emerging disease in wildlife throughout the world. The mite originates from a human ancestor and is thought to have spread to domestic and then free-living animals. Based on the recent emergence of sarcoptic mange in Australian wildlife and Aboriginal communities, it is thought that Sarcoptes scabiei was probably introduced to Australia by the Europeans and their animals. The mitochondrial genetic similarity of mites from Australian wildlife and domestic animals supports this. In Australian wildlife, sarcoptic mange has been reported in the common wombat Vombatus ursinus, southern hairy-nosed wombat Lasiorhinus latifrons, koala Phascolarctos cinereus, common ringtail possum Pseudocheirus peregrinus and in 2003 in the agile wallaby Macropus agilis. Compared with other native species, sarcoptic mange has by far its greatest impact on wombats, particularly common wombats, and is capable of causing high morbidity and mortality rates.
Epidemic viral diseases of wildlife ? sudden death in tammar wallabies, blind kangaroos, herpesviruses in pilchards ? what next?
Authors: D. Kirkland Peter
Published: April 2020

In Australia the impact of European settlement on the indigenous human population and on flora and fauna is inevitably the subject of ongoing speculation. Major changes have occurred as a result of urban and rural developments and the introduction of agricultural practices which collectively impact on the environment and ecosystems especially through land clearing, water use and modification of water courses and water catchments. From both a human and animal health perspective, the changes as viewed by the general public are perhaps not always apparent but the impacts are no less significant. A range of microbial pathogens, parasites and other pests have been introduced to populations that often have not encountered these challenges before. Our indigenous wildlife populations have not been immune from these threats. And, if we include aquatic as well as terrestrial species of ?wildlife?, and venture to our immediate coastline, in recent years there has been profound evidence of the impact that follows the introduction of an exotic pathogen.
From culture collections to biological resource centres
Authors: Kurtböke Ipek
Published: April 2020

As defined by the Organization for Economic Cooperation and Development (OECD), biological resource centres (BRCs) are an essential part of the infrastructure underpinning life sciences and biotechnology. They consist of service providers and repositories of living cells, genomes of organisms, and information relating to heredity and the functions of biological systems. BRCs contain collections of culturable organisms (e.g. genomes, plasmids, viruses, cDNAs), information on viable but not yet cultured organisms, cells and tissues, as well as databases containing molecular, physiological and structural information relevant to these collections and related bioinformatics.
UNESCO?s perspective on biological resource centres
Authors: Hoareau Lucy , Hasler Julia
Published: April 2020

The initiative of the Organisation for Economic Co-operation and Development (OECD) to establish biological resources centres (BRCs) and eventually a Global Biological Resources Centres Network (GBRCN) is a welcome one at a time when loss of biodiversity is becoming a critical concern to scientists and many governments.
Preparing for the influenza pandemic: the government response
Authors: McKinnon Moira
Published: April 2020

In February 2003, a small group of scientists and clinicians met in Sydney to map out how Australia could best respond if a case of smallpox occurred in Australia. The day was interrupted by a teleconference on the two deaths in Hong Kong of family members who had been in South China. One was confirmed to have avian influenza, H5N1, the same virus which had caused 18 cases and six deaths in Hong Kong in 1997.
Vertical Transmission, May 2006
Authors: Rood Julian
Published: April 2020

I look forward to seeing you at the ASM Annual Scientific Meeting in the Gold Coast from 2-6 July. The scientific programme is very exciting and is headed by Rubbo Orator, Professor Ruth Hall and Fenner Lecturer, A/Prof. Rick Cavicchioli, and features a plenary lecture entitled Infections & cancer ? opportunities & challenges by Australian of the Year, Professor Ian Frazer. In addition, you can learn how to communicate with the media from the American Society for Microbiology?s Communications Director, Barbara Hyde. Escape the depths of winter and join us in July for some high quality science and a little sun; it is not too late to register
Bacterial communication: when does a metabolite become a signal?
Authors: Manefield Mike , McDougald Diane , A Rice Scott , Kjelleberg Staffan
Published: April 2020

Bacterial communication has risen to prominence in microbiology as a dynamic research topic, both because of its role in microbial ecology and evolution and for the opportunity it offers to control pathogenic microbial activity. Bacterial communication has evolved from the metabolic processes of prokaryotic cellular life, in which the biosynthesis and breakdown of chemical compounds in central metabolism generates secondary metabolites with ambiguous utility in natural selection.
Regulatory issues in pandemic influenza vaccine development
Authors: Grohmann Gary
Published: April 2020

The Therapeutic Goods Administration (TGA) is responsible for the licensing of vaccines used in Australia. This includes pre-market evaluation aspects (such as assessing the quality, efficacy and safety of vaccines) and post-market aspects (such as batch release testing and the monitoring of adverse reactions). For inter-pandemic and pandemic influenza vaccines, TGA is also involved in the selection of appropriate vaccine viruses and the calibration and supply of reagents for the production of influenza vaccines. Together with industry, TGA has a responsibility to ensure that all regulatory and good manufacturing requirements (GMP) are met to ensure vaccine safety and efficacy.
Diagnosis of Chlamydia trachomatis using self-collected non-invasive specimens ? the Australian experience
Authors: N. Tabrizi Sepehr
Published: April 2020

Chlamydia trachomatis are small, non-motile, obligate intracellular bacteria that typically infect human eukaryotic columnar epithelial cells. C. trachomatis infections result in a number of diseases of worldwide public health concern, including trachoma, lymphogranuloma venereum (LGV) and urogenital infections. Chlamydia is the most common sexually transmitted bacterial pathogen worldwide and in Australia has exhibited a steady rise in prevalence 1. National notification rates of newly diagnosed chlamydia infections have increased nearly four-fold since 1994 and more than doubled since 1999.
Biobracing the future with smart microbes: towards bioindustrialisation
Authors: Kurtboke Ipek
Published: April 2020

Bioindustry has been referred to as a cluster of companies producing engineered biological products, their supporting businesses and their classification on the basis of end markets such as therapeutics, diagnostics and bio-products for agriculture and bioremediation. Bioindustry also supports high technology applications for the creation of new energy sources and linkages to microelectronics and nanotechnology.
Laboratory accidents and breaches in biosafety – they do occur!
Authors: Della-Porta Tony
Published: April 2020

In 2003 and 2004 the world became aware of three high profile microbiological incidents in Asia associated with infections with the SARS coronavirus (SARS CoV). Early in 2004 SARS was causing major disruption to many Asian countries, costing a considerable amount in lost trade and in handling the medical emergency. However, through strict quarantine measures, the disease was controlled and eradicated the virus as a cause of disease in humans (although it continues to exits in wildlife).
The Australian Chemical, Biological, Radiological and Nuclear Data Centre
Authors: Morrish Bronwyn , Wenger Eric
Published: April 2020

How well can Australia prevent and respond to an act of bioterrorism and how much do researchers in the life sciences know about the potential application of their work for hostile purposes? To further address these and other issues relating to the malicious use of hazardous substances, the Australian government has established the Australian Chemical, Biological, Radiological and Nuclear (CBRN) Data Centre.
Bacteriophage therapy: experience from the Eliava Institute, Georgia
Authors: Chanishvili Nina , Sharp Richard
Published: April 2020

The lysis of bacteria by bacteriophage was independently discovered by Frederick Twort and Felix d?Herelle but it was d?Herelle who proposed that bacteriophage might be applied to the control of bacterial diseases. Within the former Soviet Union (FSU), bacteriophage therapy was researched and applied extensively for the treatment of a wide range of bacterial infections. In the West, however, it was not explored with the same enthusiasm and was eventually discarded with the arrival of antibiotics. However, the increase in the incidence of multi-antibiotic-resistant bacteria and the absence of effective means for their control has led to increasing international interest in phage therapy and in the long experience of the Eliava Institute. The Eliava Institute of Bacteriophage, Microbiology and Virology (IBMV), which celebrates its 85th anniversary in 2008, was founded in Tbilisi in 1923 through the joint efforts of d?Herelle and the Georgian microbiologist, George Eliava.
Endemic MRSA management: is screening useful?
Authors: Spelman Denis
Published: April 2020

Endemic hospital methicillin-resistant Staphylococcus aureus (MRSA) remains a cause of significant morbidity and mortality. However, there is no universal consensus on optimal control measures. MRSA screening has been reported as a successful intervention but generally in association with a raft of other measures. Improved hand hygiene, antibiotic stewardship and the availability of isolation facilities are considered to be basic components in MRSA control. Targeted screening of high risk patients is likely to be useful for MRSA control but only if results are available in a timely manner and with resources that allow appropriate response to positive results.
Serology testing for syphilis in pregnancy: is it still relevant?
Authors: Robertson Peter W
Published: April 2020

Until the emergence of HIV and other more spectacular viral diseases, syphilis has probably been referred to more than any other infectious disease throughout history ? in theatre, literature and politics. During the 19th century, aside from being a notorious disease transmitted sexually, it was the diverse clinical and pathological forms of syphilis which led to much of this mystique and fear.
Pathogenesis of malaria in pregnancy
Authors: Meshnick Steven R , Rogerson Stephen J
Published: April 2020

Even though we have good tools to prevent and treat malaria, it remains a tragically common disease in poor countries, especially in Africa. Pregnant women are particularly susceptible to malaria, causing anaemia and poor birth outcomes. There is marked sequestration of Plasmodium falciparum-infected erythrocytes (IEs) in the placenta, but the pathogenesis of malaria in pregnancy is still incompletely understood. Both intermittent preventive therapy and insecticide-impregnated bed nets are effective protective measures, but new measures are also needed.
Intrauterine infection: preterm birth and pulmonary impact
Authors: Lahra Monica M
Published: April 2020

Acute chorioamnionitis is the histological hallmark of intrauterine infection and remains today the focus of intense, and increasing, research interest. This interest is underpinned by the association of chorioamnionitis with preterm delivery. Extreme prematurity is the fundamental, unresolved problem in perinatal medicine, has associated high morbidity and mortality, and accounts for a significant proportion of the health expenditure in the developed world. The preterm delivery rate is increasing in Australia, from 6.8% in 1991 to 8.1% in 2005. Advancement in intensive care practice has increased survival of very preterm neonates, and this has meant an increase in diseases that are directly related to prematurity, such as cerebral palsy and neonatal chronic lung disease (CLD).
Microalgal biofuel systems: Climate change, fuel supply and economic opportunities for sustainable development
Authors: Stephens Evan , Ross Ian L , Hankamer Ben , Posten Clemens , Kruse Olaf
Published: April 2020

The development of carbon neutral fuels for the future is one of the most urgent challenges facing our society for three reasons ? to minimise the effects of climate change, to protect against fuel price shocks and to provide a secure basis for economic growth.
Equine influenza in Australia
Authors: Perkins NR
Published: April 2020

A large-scale outbreak of equine influenza (EI) virus in Australia in 2007 resulted in major disruption to horse activities and related industries across the nation and particularly in the two infected states (Queensland and New South Wales). In a major test of animal health response capacity, the outbreak was successfully contained and the EI virus eradicated as a result of a coordinated national response that relied heavily on the cooperation of government and industry stakeholders. Quarantine measures have been strengthened to minimise the risk of future incursions and ensure that Australia remains free of this important and highly contagious disease.
Rabies incursion into Bali, Indonesia in 2008
Authors: Scott-Orr Helen , Putra Anak Agung Gde
Published: April 2020

Canine and human rabies cases were confirmed in Bali in late November 2008, following several months of reported outbreaks of unusual dog biting episodes and several human deaths, with clinical signs consistent with rabies. Bali had been historically free of rabies, although the disease is endemic in many other parts of Indonesia. This incursion provides a unique case study into the local spread of rabies in a naive population with no prior public awareness of the disease and the possibility of eradicating rabies from Bali before it becomes endemic. Careful study of the risk factors which were present at the time of incursion should help both Indonesia and Australia anticipate, prepare for and hopefully prevent further incursions elsewhere.
Ebola-Reston virus in pigs
Authors: Lee Johnathan
Published: April 2020

Ebolavirus Reston was detected in samples taken from pigs on two farms in the northern Philippines in mid-2008. This was the first known case of any of the filoviruses being detected in pigs anywhere in the world. Previously, filoviruses have only been isolated from humans and non-human primates, although serological evidence indicates that bats may also be infected with these viruses. Serological evidence of infection was also detected in six of 147 in-contact people tested as part of the investigation into this outbreak.
A disc test of antifungal susceptibility
Authors: Cheng Joanna , Pham Jeanette , Bell Sydney
Published: April 2020

Diagnostic laboratories are frequently requested to perform antifungal susceptibility tests on isolates recovered from systemic infections. A standard reference procedure of broth dilution was proposed by the Clinical and Laboratory Standards Institute (CLSI), but it is too labour-intensive for most clinical laboratories. CLSI also suggested a disc diffusion method, which is a cost-effective alternative method and simple to use in diagnostic microbiology laboratories. However, the method does not deal satisfactorily with the difficulty in interpretation of inhibitory zones on disc testing of those strains that show a ?trailing effect? on minimum inhibitory concentration (MIC) determination of the azole group of antifungals. Although disconcerting, trailing is regarded as an in vitro phenomenon and these strains are generally regarded as susceptible. We present a disc diffusion test for use with available antifungals, based on the Calibrated Dichotomous Sensitivity (CDS) method, used in antibiotic susceptibility testing of bacteria. The disc testing was done under predetermined optimal condition of growth, that overcame the problem of the ill-defined inhibitory zones of the azoles.
Chapter One - The need for a learned society: building a community
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

The location was Melbourne. The year was 1958. An ANZAAS Congress was underway. A small group of microbiologists got together and held a meeting. The topic for discussion was microbiology. But it was not the science of microbiology that was being debated. Rather, it was the need for a society dedicated to microbiology and to microbiologists ? the need for an organisation that would bring those working in the discipline together and further the cause of this essential and boundary-crossing science.
Biology concept assessment tools: design and use
Authors: Knight Jenny
Published: April 2020

Many recent publications have highlighted the need for, and value of, concept assessments (also called inventories) in undergraduate biology education. Current interest in such assessments is primarily due to the emergence of a community of science education researchers in biology, who both approach teaching from a scientific perspective and want to measure the potential successes of their teaching reforms. Well-designed, valid and reliable assessment tools that allow instructors to capture student learning of the main concepts of biology are becoming an essential way to inform biology instructors about what students learn in college biology courses. This review summarises the general approaches taken in creating such concept assessment tools and presents some of the ways to effectively use them.
“At the end of my course, students should be able to …”: The benefits of creating and using effective learning goals
Authors: Perkins Katherine , Smith Michelle
Published: April 2020

At the University of Colorado at Boulder (CU), several science departments ? including Molecular, Cellular, and Developmental Biology (MCDB) ? are working to improve undergraduate science education as part of the Science Education Initiative (SEI). The SEI is a 5-year project designed to support faculty-led, departmental-wide improvements in students? learning of and engagement in science. In each of the five funded departments, faculty are taking a scholarly approach to transforming their courses and introducing proven teaching practices. An important first step in course transformation has been to define explicit learning goals (also known as ?learning outcomes? or ?objectives?) for each course. In this paper, we focus on the process and benefit of writing learning goals, with specific examples from CU?s MCDB department.
Mitochondria, oxidative stress and the petite phenotype in Saccharomyces cerevisiae
Authors: Ayer Anita , Dawes Ian W , Perrone Gabriel G
Published: April 2020

Oxidative stress has long been recognised as biologically important and is increasingly implicated in a variety of phenomena, such as mutation, carcinogenesis, degenerative and other diseases, inflammation, ageing, and development. The role of the mitochondrion in oxidative stress and the production of reactive oxygen species (ROS) and other radical species is well-established, with mitochondria providing a fascinating area of study within the oxidative stress field. Mitochondria are essential organelles for the viability of all eukaryotic organisms. While mitochondria perform important processes associated with oxidative phosphorylation and energy production, and numerous other metabolic processes, such as iron sulfur cluster biogenesis, lipid and amino acid synthesis, they also appear to be the largest intracellular source of ROS in aerobic cells. The steady state concentration of O2 in the mitochondrial matrix is five- to tenfold higher than in the cytosol or nuclear space according to one estimation. Therefore, mitochondrial macromolecules such as mitochondrial DNA are particularly susceptible to oxidative damage.
Resistance to the biocidal activity of silver in burn wound dressings – is it a problem?
Authors: Merlino John , Kennedy Peter
Published: April 2020

Severe burn injuries are commonly associated with significant mortality and morbidity. A burn injury of 30% of the body surface area is associated with generalised depression of the immune system. Survival from these injuries is due to many factors, including the control of bacterial colonisation and infections leading to sepsis. Many of the organisms commonly recovered from infected patients in the burn ICU are members of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) group of pathogens recognised as the most challenging bacteria carrying multidrug (MDR) resistance facing clinicians today. Efforts to control wound burn sepsis is routinely managed by the topical application of dressings containing silver. There is concern that some microorganisms can develop resistance to the biocidal activity of silver and that this may increase due to the widespread commercial use of silver.
From the Editors
Authors: Macreadie Ian , Macreadie Johann , Macreadie Hayley
Published: April 2020

Microbiology Australia has gone through a major change this year as ASM seeks to contain costs to the Society. Of course many other journals are already online only journals so most readers will be familiar with this format. For Microbiology Australia the change means we have the opportunity to add videos, web links and virtually unlimited supplementary material. We are interested in hearing your stories of how you now use the electronic journal.
Swine flu – lessons we need to learn
Authors: Collignon Peter
Published: April 2020

Important lessons need to be learnt from the recent swine flu pandemic. Overall the population health effects of swine flu were less than a moderately severe seasonal influenza outbreak. A pandemic should not be declared unless we have both the spread of the virus but also when its virulence is above a predefined level. We need to ensure that we improve techniques to decrease the spread of infection both in the community and within our hospitals. This means improved infection control and hygiene with the use of masks, alcohol hand rubs and so on We also need to have a different approach to vaccines. Effective vaccines were produced only after the epidemic had passed and so had relatively little efficacy in preventing many infections. Mass population strategies involving vaccines and antivirals also misused large amounts of scarce medical resources.
Development and testing of the Australian pandemic influenza vaccine – a timely response
Authors: Rockman Steven , Schoofs Peter , Greenberg Michael
Published: April 2020

In April 2009 a novel virus strain appeared which would cause the first influenza pandemic of the 21st century. This pandemic was the first to occur in an era where bioinformatic technologies contributed to the response to this virus; still, the creation of a vaccine relied largely on existing egg-based technology. The ongoing threat of a H5N1 pandemic spurred the development of strategies to rapidly produce a pandemic vaccine. These plans were implemented and allowed CSL and Australia to conduct the first clinical trials and produce one of the first 2009 pandemic vaccines. However, new candidate influenza vaccine viruses often present challenges to manufacturing a new vaccine. This pandemic virus was no exception. Being in the post-pandemic phase, it is important to review lessons learned to improve our response to future pandemics. In hindsight, the production of a pandemic vaccine is similar to that of seasonal influenza vaccines, yet the urgency of the pandemic response compresses timelines. This report explores those timelines and implications for producing a pandemic vaccine for Australia.
Clinical impact of influenza – lessons learnt from the pandemic influenza A (H1N1) 2009
Authors: Dierig Alex , Khandaker Gulam , Booy Robert
Published: April 2020

Influenza is generally an acute, self-limiting, febrile illness without further complications in the majority of people. However, it can be associated with severe morbidity and mortality and the burden of the disease on society is likely to be underestimated. In 2009 an outbreak of H1N1 influenza A virus infection was detected in Mexico with further cases soon observed worldwide. Subsequently, in June 2009, the first influenza pandemic of the 21st century due to influenza A (H1N1) was declared by the World Health Organization (WHO). There were many uncertainties regarding the virulence, clinical symptoms and epidemiological features of this newly evolved influenza A strain. Over time, many similarities, but also some differences between the pandemic H1N1 influenza A and seasonal influenza were identified. We recently performed a systematic review of the literature, looking at articles published between 1 April 2009 and 31 January 2010, to identify the epidemiological and clinical features of the pandemic H1N1 influenza. In this current article we compare our findings with others from the international literature. There was more severe impact on young and healthy adults, children, pregnant women and the obese. Clinical features in general were similar between seasonal and pandemic influenza; however, there were more gastrointestinal symptoms associated with pandemic H1N1 influenza. Shortness of breath was characteristic of more severe pH1N1 2009 infection with a higher possibility of being admitted to an intensive care unit (ICU).
Microbial systematics
Authors: Kurtboke Ipek
Published: April 2020

This special issue of Microbiology Australia covers microbial systematics. In guest-editing this issue my intention has been to bring world experts together to discuss the past, present and future of microbial systematics with a view on the technical and theoretical advancements in the field. While the global debate continues on how to define ?microbial species? in the light of recent advances, expert authors contribute insights into how sound taxonomical analyses can benefit this process of redefinition.
Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification
Authors: Kampfer Peter , Glaeser Stefanie P
Published: April 2020

The initial step in prokaryote species and genera descriptions is now largely based on the 16S rRNA gene sequencing approach followed often by a very restricted additional phenotypic characterisation of the representatives of the potential novel taxa. Despite the advantages of the sequence-based approaches, there appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data. However, the biological meaning behind these sequence data is not always clear, and one should be careful with comprehensive taxonomic rearrangements until there is better insight of these data.
Bacteriophage taxonomy
Authors: Ackermann Hans W
Published: April 2020

Bacteriophages or ?phages? are viruses of prokaryotes. At least 5,360 tailed and 179 cubic, filamentous, and pleomorphic bacterial viruses have been examined in the electron microscope since the introduction of negative staining in 1959. Since at least 100 novel bacterial viruses are described every year1, the approximate number of viruses under consideration is over 6,000. Numerically, this makes bacteriophages the largest virus group known. Phages are presently classified in a hierarchical and holistic system with one order and 10 families. Over 96% of phages are tailed and contain dsDNA. The seven families of cubic, filamentous and pleomorphic phages are small and well defined. They contain ds or ss DNA or RNA. The most important developments are reclassifications of the Podoviridae and Myoviridae families of tailed phages.
The role of the public sector and philanthropy in vaccine development
Authors: Gust Ian
Published: April 2020

Vaccine development is now big business, with the global market, which is dominated by five research-based companies, growing at around 12% per annum and estimated to reach US$50 billion by 2016.
Systems biology: a new paradigm for industrial yeast strain development
Authors: Varela Cristian , Schmidt Simon A , Borneman Anthony R , Kromer Jens O , Khan Alamgir , Chambers Paul J , Wine Yeast Systems Biology Consortium The Australian
Published: April 2020

One of the key challenges for industrial yeast strain development is to obtain a thorough understanding of the biology of yeast and to apply this knowledge to develop novel strains with improved features. The detailed study of individual biological components and the use of metabolic engineering have benefited the development of industrial strains enormously; however, such approaches have failed to describe yeast behaviour in the detail required to reveal the complex interactions operating within such biological systems. How can we accurately describe the biological processes and the interactions that occur during fermentation or cell growth?
Quantification of microbial phenotypes using 13C-Fluxomics
Authors: Kromer Jens O
Published: April 2020

Systems biology is an emerging tool in microbiology that helps us to understand cellular processes and to optimise microbes for production purposes1. It strongly relies on the use of large datasets created using omics tools followed by data mining and modelling in order to gain new insights into biology. The creation of the datasets is usually comprised of genomics defining the overall capacity of a microbe, transcriptomics and proteomics as a measure of the active set of reactions within the overall capacity and more recently metabolomics as a measure of the available building blocks and (if performed quantitatively) of the thermodynamic driving forces governing the intracellular reactions. The latter can define feasibility of pathways as well as reaction reversibility, which can be important constraints for the analysis of metabolic networks. However, all these omics techniques fail to quantitatively assess the metabolic phenotype in its ultimate form: The reaction rates, or metabolic fluxes inside the cell that define the material transfer rates from one metabolite pool to another and from pathway to pathway. The ?omics technology that enables the quantification of fluxes is metabolic flux analysis, or fluxomics.
Annual ryegrass toxicity – an animal disease caused by toxins produced by a bacterial plant pathogen
Authors: Allen Jeremy
Published: April 2020

Annual ryegrass toxicity (ARGT) is an acute and often fatal neurological disease of livestock caused by consumption of annual ryegrass (Lolium rigidum) seed heads infected with the bacterium Rathayibacter toxicus (formerly Clavibacter toxicus and Corynebacterium rathayi). These toxic seed heads may be present in pasture, crop stubbles or provided feed (hay, grain, crop fines or pellets).
Food Security in Southeast Asia
Authors: Baxter Les
Published: April 2020

Food security, defined by the 1996 World Food Summit as existing ?when all people at all times have access to sufficient nutritious food to maintain a healthy and active life?, has been identified as a major issue for Southeast Asian countries. In the majority of developing countries the most effective means of ensuring food security is broad-based economic growth in agriculture. Public support for agriculture has waned significantly since the mid-1980s. Australia has been a leader in the recent resurgence of aid investment in agriculture. This has involved lifting investment in agricultural research in developing countries, through ACIAR, and AusAID programs, in particular in the Mekong countries, South Asia and Africa.
Molecular epidemiology of rotavirus in the era of vaccination
Authors: Donato Celeste
Published: April 2020

Rotavirus is the principal aetiological agent of severe acute gastroenteritis in young children worldwide. Two vaccines, Rotarix [GlaxoSmithKline] and RotaTeq [Merck], have been developed to address the large burden of disease experienced worldwide. Both vaccines have been successful in decreasing morbidity and mortality associated with rotavirus gastroenteritis. Minor fluctuations in rotavirus epidemiology have been observed since vaccine introduction. However, it is unclear whether these observations are due to selection pressures specific to vaccine introduction or due to natural genotype fluctuations.
Pathogenesis and replication of norovirus: following the mouse tail?
Authors: Hyde Jennifer , McKenzie Jason
Published: April 2020

The emergence of human noroviruses (NoV) as significant human pathogens over the last decades has highlighted the need to research and understand the replication and pathogenesis of this group of viruses. One of the major hurdles faced by researchers in this field has been the lack of a viable tissue culture system or small animal model with which to study human NoV replication. The discovery of a murine NoV in 2003 and the identification of its tropism for macrophage and dendritic cell lines has provided the opportunity to study aspects of NoV replication and pathogenesis that were previously closed to researchers.
Microorganisms: Their benefits and beyond
Authors: Kurtböke Ipek , Macreadie Ian
Published: April 2020

Most microorganisms may be associated with disease and destruction for outsiders but for us microbiologists not all microorganisms are considered ?Bad Guys? and their beneficial activities by far outnumber their detrimental aspects. In this issue of Microbiology Australia, we target those microorganisms which have served mankind with their beneficial properties either as themselves such as probiotics or through their products such as antibiotics.
"Beneficial microorganisms for sustainable agriculture"
Authors: Gupta Vadakattu VSR
Published: April 2020

Global agriculture has to double food production by 2050 in order to feed the world?s growing population and at the same time reduce its reliance on inorganic fertilisers and pesticides. To achieve this goal, there is an urgent need to harness the multiple beneficial interactions that occur between plants and microorganisms. The beneficial influences of microorganisms on plant growth include nitrogen fixation, acquisition and uptake of major nutrients, promotion of shoot and root growth, disease control or suppression and improved soil structure. Some of the commonly promoted and used beneficial microorganisms in agriculture worldwide include Rhizobia, Mycorrhizae, Azospirillum, Bacillus, Pseudomonas, Trichoderma, Streptomyces species and many more. Unravelling the biota black box using modern molecular methods is helping to find new suites of beneficial microorganisms that can help improve agricultural production worldwide.
Retraction notice to ‘Subversion of immunity by schistosomes’. [Microbiology Australia 2013, 34(3), 137–141. doi:10.1071/MA13046]
Authors: Kalinna Bernd , Walduck Anna
Published: April 2020

After due consideration, the editors of the journal and the authors of the paper agree that the paper be retracted from Microbiology Australia.
Reason: irresolvable authorship dispute.
Anaerobic bacteria
Authors: Lyras Dena , Rood Julian I
Published: April 2020

In the beginning there was no oxygen. The anaerobes ruled the earth at that time and they continue to play an important role in our oxygenated world, in food microbiology, microbial ecology and bacterial pathogenesis. Welcome to this special issue of Microbiology Australia, which is dedicated to anaerobic microbes.
Diseases of aquaculture
Authors: Buller Nicky
Published: April 2020

The value of production of aquaculture in Australia is around $990 million1 and consists of cultivation of over 40 species, most for food, but others such as pearl oysters and crocodiles are cultured for products for the fashion industry. A number of finfish are grown for food including salmon, barramundi, and silver perch, and other species include prawns, marron, abalone, oysters and mussels, whereas southern bluefin tuna are caught from the wild and farmed until they reach market size. A number of species are being investigated for aquaculture and these include octopus and sea cucumber.
Vale Andrew Butcher
Authors: Sideris Paul
Published: April 2020

It is with great sadness that I convey to you the passing of Dr Andrew Butcher. Andrew passed away peacefully on December 8 after suffering from the debilitating illness, MND. Despite the decline in his health over the last few years and dealing with the passing of Wendy, his wife, last year, Andrew remained very positive and continued to do as much as he could to catch up and celebrate life with friends, family and colleagues at every opportunity. His outlook on life was incredible right to the end.
Microbial Resources: From Functional Existence in Nature to Applications
Authors: Kurtböke İpek
Published: April 2020

Microbial Resources: From Functional Existence in Nature to Applications (Elsevier, ISBN 978-0-12-804765-1) provides an exciting interdisciplinary journey covering sustainable use of microbial resources stemming from sound understanding on their functional existence in nature, and utilising this knowledge for industrial and biotechnological applications. Examples include: (1) molecular detection, culturing and preservation of bioactive microorganisms, (2) socioeconomic value deriving from their industrial use, as well as (3) legal perspectives related to socioeconomic benefit sharing by all stakeholders, having effectively contributed to the detection, preservation and exploitation of such microbiological material.
Tubulin tails and their modifications regulate protein diffusion on microtubules
Authors: Bigman Lavi S. , Levy Yaakov
Published: April 2020

Microtubules (MTs) are essential components of the eukaryotic cytoskeleton that serve as “highways” for intracellular trafficking. In addition to the well-known active transport of cargo by motor proteins, many MT-binding proteins seem to adopt diffusional motility as a transportation mechanism. However, because of the limited spatial resolution of current experimental techniques, the detailed mechanism of protein diffusion has not been elucidated. In particular, the precise role of tubulin tails and tail modifications in the diffusion process is unclear. Here, using coarse-grained molecular dynamics simulations validated against atomistic simulations, we explore the molecular mechanism of protein diffusion along MTs. We found that electrostatic interactions play a central role in protein diffusion; the disordered tubulin tails enhance affinity but slow down diffusion, and diffusion occurs in discrete steps. While diffusion along wild-type MT is performed in steps of dimeric tubulin, the removal of the tails results in a step of monomeric tubulin. We found that the energy barrier for diffusion is larger when diffusion on MTs is mediated primarily by the MT tails rather than the MT body. In addition, globular proteins (EB1 and PRC1) diffuse more slowly than an intrinsically disordered protein (Tau) on MTs. Finally, we found that polyglutamylation and polyglycylation of tubulin tails lead to slower protein diffusion along MTs, although polyglycylation leads to faster diffusion across MT protofilaments. Taken together, our results explain experimentally observed data and shed light on the roles played by disordered tubulin tails and tail modifications in the molecular mechanism of protein diffusion along MTs.
Outer membrane vesicles catabolize lignin-derived aromatic compounds in
Pseudomonas putida
KT2440
Authors: Salvachúa Davinia , Werner Allison Z. , Pardo Isabel , Michalska Martyna , Black Brenna A. , Donohoe Bryon S. , Haugen Stefan J. , Katahira Rui , Notonier Sandra , Ramirez Kelsey J. , Amore Antonella , Purvine Samuel O. , Zink Erika M. , Abraham Paul E. , Giannone Richard J. , Poudel Suresh , Laible Philip D. , Hettich Robert L. , Beckham Gregg T.
Published: April 2020

Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic–catabolic bacteria:
Pseudomonas putida
KT2440,
Rhodoccocus jostii
RHA1, and
Amycolatopsis
sp. ATCC 39116.
P. putida
cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
Gene drive and resilience through renewal with next generationCleave and Rescueselfish genetic elements
Authors: Oberhofer Georg , Ivy Tobin , Hay Bruce A.
Published: April 2020

Significance

Gene drive can spread beneficial traits through populations, but will never be a one-shot project in which one genetic element provides all desired modifications, for an indefinitely long time. Here, we show that gene drive-mediated population modification inDrosophilacan be overwritten with new content while eliminating old, usingCleave and Rescue(ClvR) selfish genetic elements. The ability to carry out cycles of modification that create and then leave behind a modest genetic footprint while entering and exiting a population provides important points of control. It makes possible the replacement of broken elements, upgrades with new elements that better carry out their tasks, and/or provide new functions, all while promoting the removal of modifications no longer needed.
Nominalisations in scientific English
Authors: Hao Jing
Published: April 2020

This paper examines nominalisation in scientific discourse in English, focusing on a distinction between what I
will refer to as ‘live’ and ‘dead’ grammatical metaphors. Live metaphors refer to a nominal realisation of an ideational discourse
semantic figure; dead metaphors are found in the same nominalisations as live metaphors, but they realise an entity rather than a
figure. The distinction is made by drawing on a tristratal approach that is informed by Systemic Functional Linguistics and that
considers nominalisation simultaneously from the perspectives of field, discourse semantics, and lexicogrammar. Although the paper
focuses on nominalisation, it illustrates a broader line of argumentation that can be extended to the analysis of ideational
discourse semantic meanings in general.
More than just a modal particle
Authors: Forker Diana
Published: April 2020

Modal particles have been intensively studied in German and a few other European languages, but investigations of modal particles from little-known languages are rare. This paper examines in detail the morphosyntactic and the semantic properties of the Sanzhi Dargwa (Nakh-Daghestanian) modal particle =q’al. It is shown that the particle possesses the morphosyntactic properties that are commonly assumed for modal particles. The particle is then analyzed as presupposition trigger that interacts with focus and marks clauses as declarative sentences. It triggers two presuppositions, namely uncontroversiality and contrast/correction. Furthermore, it can express finiteness. The analysis suggests that accounting for modal particles as grammatical rather than lexical items with head status seems promising for further research.
Iran Linguistic Atlas Project (ILA): Past and Present
Authors: Akhlaghi Faryar
Published: April 2020

Iran Linguistic Atlas (ILA), funded by the Research Institute for Cultural Heritage and Tourism (RICHT), is a research project for mapping the linguistic diversity of Iran. The project is aimed at recording unified and comparable data from every spoken dialect of Iran’s rural areas and producing self-organized colored maps of this diversity using a specialized software program. Its initial phase began around the mid-1970s in the form of a joint project by the then Iranian Academy of Language and the National Geography Organization. In 2001, the documented data was handed over to the Cultural Heritage Organization, to be saved and expanded. The Iran Linguistic Atlas has now been redefined as an automatic linguistic atlas with the capability of producing self-organizing colored maps according to the operator’s choices. In this article, the ILA, its background and the state of its current phase is introduced. The nature of its data, its earlier and recent field methods, its audiotapes, digital databases and computer databases of phonetic transcriptions are described. In addition, ILA software program is presented and its capability for creating automatic colored maps is discussed thoroughly.
One Year Mortality of Patients Treated with Naloxone for Opioid Overdose by Emergency Medical Services
Authors: Weiner Scott G. , Baker Olesya , Bernson Dana , Schuur Jeremiah D.
Published: April 2020

Study objective: Prehospital use of naloxone for presumed opioid overdose has increased markedly in recent years because of the current opioid overdose epidemic. In this study, we determine the 1-year mortality of suspected opioid overdose patients who were treated with naloxone by EMS and initially survived. Methods: This was a retrospective observational study of patients using three linked statewide datasets in Massachusetts: emergency medical services (EMS), a master demographics file, and death records. We included all suspected opioid overdose patients who were treated with naloxone by EMS. The primary outcome measures were death within 3 days of treatment and between 4 days and 1 year of treatment. Results: Between July 1, 2013 and December 31, 2015, there were 9734 individuals who met inclusion criteria and were included for analysis. Of these, 807 (8.3% (95% confidence interval (CI) 7.7–8.8%)) died in the first 3 days, 668 (6.9% (95% CI 6.4–7.4%)) died between 4 days and 1 year, and 8259 (84.8% (95% CI 84.1–85.6%)) were still alive at 1 year. Excluding those who died within 3 days, 668 of the remaining 8927 individuals (7.5% (95% CI 6.9–8.0%)) died within 1 year. Conclusion: The 1-year mortality of those who are treated with naloxone for opioid overdose by EMS is high. Communities should focus both on primary prevention and interventions for this patient population, including strengthening regional treatment centers and expanding access to medication for opioid use disorder.