Atlas of vertebrate decay: a visual and taphonomic guide to fossil interpretation

Like many other important evolutionary transitions, our knowledge of the origin of vertebrates is limited to windows of exceptional preservation of soft‐bodied fossils. Unfortunately, these fossils are rare and have been subjected to complex taphonomic filters including decay, collapse and distortion. To maximize our ability to utilize these crucial fossils to reconstruct the timing and sequence of evolutionary events, we are in the need of a robust taphonomic framework with in which to interpret them. Here, we report the results of a series of experiments designed to examine patterns of transformation and loss during decay of important anatomical characters of chordates and primitive vertebrates (ammocoete, adult lamprey, hagfish, juvenile chondrichthyans and a non‐vertebrate chordate, Branchiostoma). Complex and repeated patterns of transformation during decay are identified and figured for informative character complexes including eyes, feeding apparatus, skull and brain, muscles, branchial apparatus, axial structures, viscera, heart and fins. The resulting data regarding character decay and relative loss serve as a guide to recognition and interpretation of the anatomy of non‐biomineralized fossil vertebrates. The methods and techniques outlined are eminently applicable to other soft‐bodied groups and present a new way to interpret the exceptionally preserved fossil record.     

Isavuconazole: A Comprehensive Review of Spectrum of Activity of a New Triazole

Isavuconazole is a new triazole currently undergoing phase III clinical trials. This compound has shown in vitro activity against a large number of clinically important yeasts and moulds including Aspergillus spp., Fusarium spp., Scedosporium spp., Candida spp., the Zygomycetes and Cryptococcus spp. Similar to voriconazole, reduced in vitro activity is seen against Histoplasma capsulatum. In vivo efficacy has been demonstrated in murine models of invasive aspergillosis and candidiasis. Additionally, there are several potential pharmacokinetic and drug–drug interaction advantages of this compound over existing antifungal agents. This review summarizes existing data that has been either published or presented at international symposia.     

The roar of the lionfishes Pterois volitans and Pterois miles

Through the analysis of acoustic recordings of captive Pterois spp., this study has confirmed anecdotal evidence that Pterois spp. are soniferous. This report of sound production in Pterois spp. provides the foundation for future research into their specific acoustic capabilities including sound production mechanisms, the role of social behaviour and applied techniques for controlling and monitoring invasive Pterois spp. in the tropical and temperate western Atlantic Ocean.     

Host plant resistance against broomrapes (Orobanche spp.): defence reactions and mechanisms of resistance

Over 4000 species of angiosperms are able to directly invade and parasitise other plants, but only very few are weedy and parasitise cultivated plants. Together with the witchweeds (Striga spp.) and dodders (Cuscuta spp.), the broomrapes (Orobanche spp.) affect important crops causing complete yield loses with severe infestations. Genetic resistance to parasitisation remains as one of the most desirable components in an integrated control strategy. However, breeding for resistance is a difficult task and many aspects of the host/parasite interaction remain unknown. In the present work, we review the cytological and cytochemical studies investigating the mechanisms of resistance involved in the process leading to an incompatible host–parasite interaction. We have attempted to identify the main gaps and problems related to such studies with parasitic plants and present an in‐depth review of histochemical techniques used to assess mechanisms of resistance against these parasitic plants. Furthermore, we discuss future research directions and novel techniques and finally, how such techniques can be applied and incorporated within a breeding programme.     

A large family of anti‐activators accompanying XylS/AraC family regulatory proteins

AraC Negative Regulators (ANR) suppress virulence genes by directly down‐regulating AraC/XylS members in Gram‐negative bacteria. In this study, we sought to investigate the distribution and molecular mechanisms of regulatory function for ANRs among different bacterial pathogens. We identified more than 200 ANRs distributed in diverse clinically important gram negative pathogens, including Vibrio spp., Salmonella spp., Shigella spp., Yersinia spp., Citrobacter spp., enterotoxigenic (ETEC) and enteroaggregative E. coli (EAEC), and members of the Pasteurellaceae. By employing a bacterial two hybrid system, pull down assays and surface plasmon resonance (SPR) analysis, we demonstrate that Aar (AggR‐activated regulator), a prototype member of the ANR family in EAEC, binds with high affinity to the central linker domain of AraC‐like member AggR. ANR‐AggR binding disrupted AggR dimerization and prevented AggR‐DNA binding. ANR homologs of Vibrio cholerae, Citrobacter rodentium, Salmonella enterica and ETEC were capable of complementing Aar activity by repressing aggR expression in EAEC strain 042. ANR homologs of ETEC and Vibrio cholerae bound to AggR as well as to other members of the AraC family, including Rns and ToxT. The predicted proteins of all ANR members exhibit three highly conserved predicted α‐helices. Site‐directed mutagenesis studies suggest that at least predicted α‐helices 2 and 3 are required for Aar activity. In sum, our data strongly suggest that members of the novel ANR family act by directly binding to their cognate AraC partners.     

Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)

In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluorescence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four‐membrane‐bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus‐encoded large subunit rRNA genes showed eight distinct lineages for apochlorotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle.     

Microarray Analyses of Shrimp Immune Responses

Shrimp aquaculture is one of the major food-producing industries in the world. However, it is being impacted by several problems including diseases, antibiotic use, and environmental factors. The extent of the effects of these problems in the immune system of the shrimp at the molecular level is just beginning to be understood. Here, we review the gene expression profile of shrimp in response to some of these problems using the high-throughput microarray analysis, including white spot syndrome virus, yellow head virus, Vibrio spp., peptidoglycan, oxytetracycline, oxolinic acid, salinity, and temperature.     

Metal complexes as optical probes for DNA sensing and imaging

Transition and lanthanide metal complexes have rich photophysical properties that can be used for cellular imaging, biosensing and phototherapy. One of the applications of such luminescent compounds is the detection and visualisation of nucleic acids. In this brief review, we survey the recent literature on the use of luminescent metal complexes (including Re^I, Ru^II, Os^II, Ir^III, Pt^II, Eu^III and Tb^III) as DNA optical probes, including examples of compounds that bind selectively to non-duplex DNA topologies such as quadruplex, i-motif and DNA mismatches. We discuss the applications of metal-based luminescent complexes in cellular imaging, including time-resolved microscopy and super-resolution techniques. Their applications in biosensing and phototherapy are briefly mentioned in the relevant sections.     

The developmental expression of fluorescent proteins in organotypic hippocampal slice cultures from transgenic mice and its use in the determination of excitotoxic neurodegeneration

Transgenic mice, expressing fluorescent proteins in neurons and glia, provide new opportunities for real-time microscopic monitoring of degenerative and regenerative structural changes. We have previously validated and compared a number of quantifiable markers for neuronal damage and cell death in organotypic brain slice cultures, such as cellular uptake of propidium iodide (PI), loss of microtubule-associated protein 2 (MAP2), Fluoro-Jade (FJ) cell staining, and the release of cytosolic lactate dehydrogenase (LDH). An important supplement to these markers would be data on corresponding morphological changes, as well as the opportunity to monitor reversible changes or long-term effects in the event of minor damage. As a first step, we present: a) the developmental expression in organotypic hippocampal brain slice cultures of transgenic fluorescent proteins, useful for the visualisation of neuronal subpopulations and astroglial cells; and b) examples of excitotoxic, glutamate receptor-induced degeneration of hippocampal CA1 pyramidal cells, with corresponding astroglial reactivity in such cultures. The slice cultures were set up according to standard techniques, by using one-week old pups from four transgenic mouse strains which express fluorescent proteins in their neurons and/or astroglial cells. From the time of explantation, and subsequently for up to nine weeks in culture, the transgenic neuronal fluorescence displayed the expected characteristics of a developmental, in vivo-like increase, including both the number and localisation of cells, as well as the intensity of fluorescence. At that stage and later, the transgenic fluorescence clearly permitted the visualisation of cell bodies, larger and smaller dendritic branches, spines and axons. In separate experiments, with a 24-hour exposure of matured sliced cultures to 100 microM of the glutamate agonist, N-methyl-D-aspartate (NMDA), we observed, by time-lapse recording, a gradual, but rapid loss of fluorescent CA1 pyramidal cells, accompanied by astrogliosis of transgene fluorescent astroglial cells. Based on these results, we consider that organotypic brain slice cultures from transgenic mice, with fluorescent neurons and glia, combined with detailed visualisation by time-lapse fluorescence microscopy, have great potential for investigating both major irreversible and minor reversible structural changes in neurons and glia, induced by neurotoxins and other neurodegenerative compounds and conditions.     

Infection and Colonization of Sugar Cane and Other Graminaceous Plants by Endophytic Diazotrophs

Agriculturally important grasses such as sugar cane (Saccharum sp.), rice (Oryza sativa), wheat (Triticum aestivum) sorghum (Sorghum bicolor), maize (Zea mays), Panicum maximum, Brachiaria spp., and Pennisetum purpureum contain numerous diazotrophic bacteria, such as, Acetobacter diazotrophicus, Herbaspirillum spp., Azospirillum spp. These bacteria do not usually cause disease symptoms in the plants with which they are associated and the more numerous of them, for example, Herbaspirillum spp. and A. diazotrophicus, are obligate or facultative endo-phytes that do not survive well (or at all) in native soil; these are thought to be spread from plant generation to plant generation via seeds, vegetative propagation, dead plant material, and possibly by insect sap feeders. By contrast, Azospirillum spp. are not wholly endophytic but are root-associated, soil-dwelling bacteria that are also often found within plants, probably entering host plants via seeds or via wounds/cracks at lateral root junctions. Endophytic diazotrophs have been isolated from a number of grasses in which significant biological N₂ fixation (BNF) has been demonstrated, particularly Brazilian sugar cane varieties, but also in rice, maize, and sorghum. However, although the endophytic diazotrophs are held to be the causative agents of the observed BNF, direct evidence for this is lacking. Therefore, in this review we examine probable sites of bacterial multiplication and/or BNF within endophyte-containing grasses and discuss these in terms of potential benefits (or not) to both host plants and bacteria. In particular, we examine how potentially large numbers of bacteria, especially Herbaspirillum spp., A. diazotrophicus, and Azospirillum spp., can exist extracellularly within non-specialized (for symbiotic purposes) regions such as xylem vessels and intercellular spaces. The processes of infection and colonization of various grasses (particularly sugar cane) by diazotrophic endophytes are also described, and these are compared with those of important (nondiazotrophic) endophytic sugar cane pathogens such as Clavibacter xyli subsp. xyli and Xanthomonas albilineans.     

Proteomic studies in biomedically and industrially relevant fungi

Historically, the proteomic investigation of filamentous fungi has been restrained by difficulties associated with efficient protein extraction and the lack of extensive fungal genome sequence databases. The advent of robust protein extraction and separation technologies, combined with protein mass spectrometry and emerging genome sequence data, is leading to the emergence of extensive new knowledge on the nature of these organisms. In this review, we discuss some recent technological advances and their role in exploring the proteome of Aspergillus spp., along with other biotechnologically relevant fungi.     

Ecology and diversity of waxcap (Hygrocybe spp.) Fungi

Summary

Members of the genus Hygrocybe are ubiquitous and colourful components of many undisturbed and nutrient-poor grasslands in the UK. Through a number of detailed surveys of the distribution of Hygrocybe spp. and of genera showing similar patterns of occurrence (e.g. Clavaria spp., Entoloma spp., Geoglossum spp.) a picture is gradually emerging of the more important ‘waxcap grassland’ sites, and of those species in greatest need of protection. Waxcap fungi are far from ideal experimental organisms which explains why so little has been published about their biology and ecology. They cannot be cultured on laboratory media and the correct conditions for inducing spores of most species to germinate have yet to be established. Nevertheless approaches such as isotope ratio mass spectrometry and the use of molecular biology techniques are beginning to provide an insight into the role played by these organisms in grassland ecosystems, and why they are so adversely affected by many agricultural practices. Current field experiments at various sites including Sourhope near Kelso will also permit investigations into waxcap ecology to be correlated with parallel studies of other members of the soil biota.     

The little bacteria that can – diversity,genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase-encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments.     

Biofilms as a microbial hazard in the food industry: A scoping review

Biofilms pose a serious public health hazard with a significant economic impact on the food industry. The present scoping review is designed to analyse the literature published during 2001–2020 on biofilm formation of microbes, their detection methods, and association with antimicrobial resistance (if any). The peer-reviewed articles retrieved from 04 electronic databases were assessed using PRISMA-ScR guidelines. From the 978 preliminary search results, a total of 88 publications were included in the study. On analysis, the commonly isolated pathogens were Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., Escherichia coli, Bacillus spp., Vibrio spp., Campylobacter jejuni and Clostridium perfringens. The biofilm-forming ability of microbes was found to be influenced by various factors such as attachment surfaces, temperature, presence of other species, nutrient availability etc. A total of 18 studies characterized the biofilm-forming genes, particularly for S. aureus, Salmonella spp., and E. coli. In most studies, polystyrene plate and/or stainless-steel coupons were used for biofilm formation, and the detection was carried out by crystal violet assays and/or by plate counting method. The strain-specific significant differences in biofilm formation were observed in many studies, and few studies carried out analysis of multi-species biofilms. The association between biofilm formation and antimicrobial resistance was not clearly defined. Further, viable but non-culturable form of the foodborne pathogens is posing an unseen (by conventional cultivation techniques) but potent threat to the food safety. The present review recommends the need for carrying out systematic surveys and risk analysis of biofilms in food chain to highlight the evidence-based public health concerns, especially in regions where microbiological food hazards are quite prevalent.     

Dematiaceous fungal pathogens isolated from nature

This study was conducted to demonstrate the presence of pathogenic dematiaceous fungi in nature. Using hamster and mouse inoculation techniques, 43 isolates of dematiaceous fungi were recovered from 39 samples of woody plant material and soil from the Virginia environment. Thirteen species were identified and included 4 Phialophora spp., 3 Cladosporium spp., 2 Exophiala spp., Sporothrix sp., Wangiella dermatitidis, Bispora betulina, and Scytalidium lignicola. Evidence is presented for the first isolations of C. trichoides from nature in the United States; these isolates proved to be pathogenic for mice in which they produced disease and death in a course similar to that seen in man. Natural isolates of Phialophora verrucosa, Phialophora repens, Exophiala jeanselmei, and Wangiella dermatitidis were identical to those species isolated from man using the following criteria: morphology, 12% gelatin reaction, and survival in laboratory animals.     

Are we overestimating risk of enteric pathogen spillover from wild birds to humans?

Enteric illnesses remain the second largest source of communicable diseases worldwide, and wild birds are suspected sources for human infection. This has led to efforts to reduce pathogen spillover through deterrence of wildlife and removal of wildlife habitat, particularly within farming systems, which can compromise conservation efforts and the ecosystem services wild birds provide. Further, Salmonella spp. are a significant cause of avian mortality, leading to additional conservation concerns. Despite numerous studies of enteric bacteria in wild birds and policies to discourage birds from food systems, we lack a comprehensive understanding of wild bird involvement in transmission of enteric bacteria to humans. Here, we propose a framework for understanding spillover of enteric pathogens from wild birds to humans, which includes pathogen acquisition, reservoir competence and bacterial shedding, contact with people and food, and pathogen survival in the environment. We place the literature into this framework to identify important knowledge gaps. Second, we conduct a meta‐analysis of prevalence data for three human enteric pathogens, Campylobacter spp., E. coli, and Salmonella spp., in 431 North American breeding bird species. Our literature review revealed that only 3% of studies addressed the complete system of pathogen transmission. In our meta‐analysis, we found a Campylobacter spp. prevalence of 27% across wild birds, while prevalence estimates of pathogenic E. coli (20%) and Salmonella spp. (6.4%) were lower. There was significant bias in which bird species have been tested, with most studies focusing on a small number of taxa that are common near people (e.g. European starlings Sturnus vulgaris and rock pigeons Columba livia) or commonly in contact with human waste (e.g. gulls). No pathogen prevalence data were available for 65% of North American breeding bird species, including many commonly in contact with humans (e.g. black‐billed magpie Pica hudsonia and great blue heron Ardea herodias), and our metadata suggest that some under‐studied species, taxonomic groups, and guilds may represent equivalent or greater risk to human infection than heavily studied species. We conclude that current data do not provide sufficient information to determine the likelihood of enteric pathogen spillover from wild birds to humans and thus preclude management solutions. The primary focus in the literature on pathogen prevalence likely overestimates the probability of enteric pathogen spillover from wild birds to humans because a pathogen must survive long enough at an infectious dose and be a strain that is able to colonize humans to cause infection. We propose that future research should focus on the large number of under‐studied species commonly in contact with people and food production and demonstrate shedding of bacterial strains pathogenic to humans into the environment where people may contact them. Finally, studies assessing the duration and intensity of bacterial shedding and survival of bacteria in the environment in bird faeces will help provide crucial missing information necessary to calculate spillover probability. Addressing these essential knowledge gaps will support policy to reduce enteric pathogen spillover to humans and enhance bird conservation efforts that are currently undermined by unsupported fears of pathogen spillover from wild birds.     

Auditory anatomy of beaked whales and other odontocetes: Potential for cochlear stimulation via a “vibroacoustic duct mechanism”

Computed tomography (CT) and microcomputed tomography (microCT) were used to examine the structures involved in cochlear stimulation in odontocetes and terrestrial mammals. Cranial CT examined the osseous attachment of the skull to the tympanoperiotic complex (TPC) and the path of the endocranial foramen of the vestibulocochlear nerve (EFVN), which was assumed to contain the perilymphatic duct. Additional CTs of TPC were taken postextraction to examine the gross morphology of this structure. MicroCT was used to examine the acoustic windows of the cochlea, including the round and oval windows and the apertures of the cochlear and vestibular aqueducts. Cranial CT scans demonstrated an osseous connection between the skull and TPC in beaked whales and Physeter macrocephalus. EFVN traveled through a greater length of cranial bone and communicated more closely with the periotic bone in beaked whales than in other species. Ziphius cavirostris was observed to have a reduced medial sulcus of the mallear ridge (MSMR) and tympanic plate and an enlarged aperture of the cochlear aqueduct, respectively. The potential significance of these findings, including the role of the perilymphatic duct as a novel route of cochlear stimulation referred to as the “vibroacoustic duct mechanism,” are discussed.     

近十年中国重要食药用菌研究进展

食用菌跻身我国第五大农作物,我国已经成为名副其实的食药用菌大国。本文对近十年来食药用菌重要种类名称变更、人工培植或栽培技术的突破和基因组学研究的进展进行了综述。随着分子系统学研究的深入,灵芝、黑木耳、毛木耳、桑黄等重要种类的名称得到更正和完善;冬虫夏草、羊肚菌、暗褐网柄牛肝菌等难栽培种类在全世界范围内首次实现人工栽培;大多数常见食药用菌种类完成了基因组解析。分析了分类和系统发育研究、生物学研究、组学研究与食药用菌产业发展的关系,基础研究促进食药用菌产业发展,同时产业发展为基础研究提出更多的科学问题。     

Growth of cranial synchondroses and sutures requires polycystin-1

In vertebrates, coordinated embryonic and postnatal growth of the craniofacial bones and the skull base is essential during the expansion of the rostrum and the brain. Identification of molecules that regulate skull growth is important for understanding the nature of craniofacial defects and for development of non-invasive biologically based diagnostics and therapies.Here we report on spatially restricted growth defects at the skull base and in craniofacial sutures of mice deficient for polycystin-1 (Pkd1). Mutant animals reveal a premature closure of both presphenoid and sphenooccipital synchondroses at the cranial base. Furthermore, knockout mice lacking Pkd1 in neural crest cells are characterized by impaired postnatal growth at the osteogenic fronts in craniofacial sutures that are subjected to tensile forces. Our data suggest that polycystin-1 is required for proliferation of subpopulations of cranial osteochondroprogenitor cells of both mesodermal and neural crest origin during skull growth. However, the Erk1/2 signalling pathway is up-regulated in the Pkd1-deficient skeletal tissue, similarly to that previously reported for polycystic kidney.