The Biology of Fungi

Fungi are found ubiquitously in the environment such as soil, water, and food. There are an estimated 1.5 million fungal species worldwide, although this number is felt to be grossly underestimated and is regularly updated. Of these vast numbers, around 500 fungi to date have been implicated in human disease. As opposed to bacteria, which are prokaryotes, fungi are eukaryotes, meaning they have a well-defined nucleus and have membrane- bound organelles in the cytoplasm, including an endoplasmic reticulum and a golgi apparatus. In 1969, the scientist R. H. Whittaker first proposed that organisms be classified into five kingdoms: Monera (Bacteria), Protista (Algae and Protozoans), Plantae (Plants), Mycetae (Fungi), and Animalia (Animals). Since then, there have been dramatic changes to the classifications of fungi, largely due to the appliance of phylogenetic molecular techniques. This has resulted in variances to the number of phylums, and the species assigned to them. Table 3.1 shows the seven phyla of the Fungi Kingdom. The majority of fungi pathogenic to humans inhabit the Ascomycota and Basidiomycota phyla. Fungi used to be dually named if they had a pleomorphic life cycle with sexual/ asexual stages (teleomorph/ anamorph, respectively), which meant that fungi often had two names and were classed differently. This practice was discontinued in January 2013 after the International Commission on the Taxonomy of Fungi decided that a ‘one fungus, one name’ approach should be followed. Fungi can be unicellular (yeast) or multicellular (fungi). Yeasts may look globose in nature when grown, whereas multicellular fungi grow as tubular, filamentous material called hyphae that can create a branching, hyphal network called a mycelium. Hyphae may have septa that cross their walls or be nonseptate, which is a method of differentiating fungi. An early hyphal outgrowth from a spore is called a germ tube. The germ tube test can be used to differentiate the yeasts Candida albicans and Candida dubliniensis from other Candida species. The fungal cell wall is composed of chitin and glucans, which are different components to the human cell wall. This means that they can be an effective target for antifungal therapy.

A Case of Intraocular Erosion and Intrusion by an Arruga Suture

Purpose: To report a case of intraocular erosion and intrusion by an Arruga suture. Case Report: This study involved a 62-year-old male who had undergone scleral buckling surgery 40 or more years ago at another hospital for rhegmatogenous retinal detachment, as well as trabeculectomy 20 years ago for primary open-angle glaucoma, in his left eye at the same hospital. However, he recently became aware of blurred vision in that eye. Upon examination, iritis was observed in the anterior portion of his left eye, as well as a great number of pigment cell keratoprecipitates on the posterior surface of the cornea. In the ocular fundus, extensive atrophy of the retinal pigment epithelium and partial hyperpigmentation was observed, accompanied by subretinal strands, yet the retina remained attached. Around the entire peripheral area of the retina we observed a ring-shaped protrusion, but we also saw a shiny, filamentous material in the vitreous cavity that penetrated the sclera and choroid, completely extending from the 4- to 8-o'clock position of the scleral buckle protrusion. To treat the iritis in the patient's left eye, we began to administrate low-concentration steroid eye drops, after which the inflammation disappeared. Conclusion: In this study, we experienced a case of intraocular erosion and intrusion by an Arruga suture, and opted to treat the patient with steroid eye drops and conservative follow-up observations unless retinal redetachment and/or vitreous hemorrhage occurs.

ON THE DISCOVERY OF A LARGE MICROBIAL COMMUNITY LIVING IN THE SOFT BOTTOMS OF THE CONTINENTAL SHELF OFF CHILE AND PERU

In a benthic macrofaunal survey of the continental shelf of northern Chile a peculiar filamentous material was collected in grab and dredge samples of greenish, foul smelling sediment from depths of 50 to 280 m (ref. 1). In reporting the results emphasis was placed, however, on the fact that a virtually iazoic* bottom had beenfound between depths of 50 to 400 m. Average biomass was only 0.17 g (wet weight) /m2 , with 6.6 individuals /m2*. The distribution of the azoic sediments coincided with low oxygen concentrations in the water above (ref. 2). The author again found white filamentous material while sampling the benthos off the Bay of Concepcion and the Gulf of Arauco, in central Chile. These findings together with the casual observation of filaments in the mouth parts of the commercially important galatheid shrimp Pleuroncodes mondon, initiated new efforts to learn about this material and its possible ecological significance.

Purple Prairie Clover (Dalea purpurea Vent) Reduces Fecal Shedding of Escherichia coli in Pastured Cattle

A 3-year (2009 to 2011) grazing study was conducted to assess the effects of purple prairie clover (PPC; Dalea purpurea Vent) on fecal shedding of total Escherichia coli in cattle. Three pasture types were used in the experiment: bromegrass (Check), mixed cool season grasses with PPC (Simple), and mixed cool and warm grasses with PPC (Complex). Pastures were rotationally grazed during a summer and fall grazing period. PPC was grazed in summer at the vegetative or early flower stage and at the flower or early seed stage during the fall. Fecal samples were collected for enumeration of E. coli and chemical analyses. Forage samples were collected throughout grazing for analysis. Condensed tannins (CT) were only detected in Simple and Complex pastures that contained PPC, with higher concentrations found in the fall than in the summer. Fecal counts of E. coli in cattle grazing Simple and Complex pastures linearly decreased (P < 0.05) over summer to fall in all 3 years, an outcome not observed in cattle grazing the Check pasture. Across the three grazing seasons, fecal E. coli was lower (P < 0.05) in cattle grazing Simple and Complex pastures than in those grazing the Check pasture during the fall. During the fall, feces collected from cattle grazing the Check pasture had higher (P < 0.05) values for pH, N, NH3-N, total volatile fatty acids, and branched-chain volatile fatty acids, but a lower (P < 0.05) acetate:propionate ratio than feces collected from cattle grazing Simple or Complex pastures. In a second experiment, two strains of E. coli were cultured in M9 medium containing 25 to 200 μg/ml of PPC CT. Growth of E. coli was linearly (P < 0.01) reduced by increasing levels of PPC CT. Scanning electron micrographs showed electron-dense filamentous material associated with the outer membrane of E. coli cells exposed to CT. Incorporation of PPC into forage reduced the fecal shedding of E. coli from grazing cattle, likely due to the anti–E. coli properties of PPC CT.

Idiopathic Complex Polysaccharide Storage Disease in an Abyssinian Cat

A glycogen storage disease affecting primarily the skeletal muscle and, to a lesser degree, the cardiac muscle, spinal cord, and brain was diagnosed in a 10-year-old neutered Abyssinian cat with a 4-year history of paresis progressing to acute paralysis. Microscopically, these tissues contained inclusions that were pale basophilic in hematoxylin and eosin-stained slides, diastase resistant, periodic acid-Schiff positive, and blue-to-almost black with iodine stain. By transmission electron microscopy, the inclusions consisted of cytosolic, usually sharply demarcated, nonmembrane-bound deposits of finely granular and filamentous material. on the basis of the structural and histochemical staining characteristics, the inclusions were believed to be aggregates of abnormally stored, unbranched glycogen. A defect in glucose metabolism is suspected to be the underlying pathologic process, but an exact cause remains elusive.

First Forty-Eight Hours of Developing Otitis Media: An Experimental Study

The early inflammatory changes in the tympanic membrane were explored in 2 rat models. Acute otitis media was induced by instillation of Streptococcus pneumoniae type 3 into the middle ear cavity, and otitis media with effusion was induced by blockage of the eustachian tube. Otomicroscopic examination was performed before the rats were painlessly sacrificed at 3, 6, 9, 12, 18, 24, or 48 hours after initiation of the otitis media conditions. The tympanic membrane was studied by light and electron microscopy. Both acute otitis media and otitis media with effusion caused early inflammatory changes of the tympanic membrane, and the pars flaccida was the portion that reacted first. The inflammatory alterations were most pronounced in the acute otitis media model. The course of inflammation showed a bimodal pattern with an early deposition of a filamentous material with a band pattern, typical of fibrin. Despite a fluid-filled middle ear cavity, the inflammatory changes in the otitis media with effusion model were moderate, as was consistent with the clinical appearance of the tympanic membrane.

Complex Polysaccharide Inclusions in Skeletal Muscle Adjacent to Sarcomas in Two Dogs

Inclusions of periodic acid-Schiff-positive, amylase resistant material were found within skeletal muscle fibers adjacent to an osteosarcoma in the proximal femur of an 8-year-old intact female Cocker Spaniel dog (dog No. 1) and adjacent to a synovial cell sarcoma of the stifle joint in a 7-year-old spayed female Bouvier des Flandres dog (dog No. 2). Inclusions were pale blue-gray with hematoxylin and eosin stain and formed irregular inclusions, replacing up to approximately 80% of the fiber diameter. Inclusions from dog No. 2 were of non-membrane-bound granular to filamentous material that occasionally formed discrete, elongate electrondense masses. The features of these inclusions were similar to those of materials previously described as complex polysaccharide, polyglucosan bodies, amylopectin, and Lafora bodies. Evidence for a generalized metabolic disorder was not found in these two dogs, suggesting that storage of complex polysaccharide can occur as a relatively nonspecific response to metabolic alterations in skeletal muscle in a variety of conditions.

Overlapping functions of lysosomal acid phosphatase (LAP) and tartrate-resistant acid phosphatase (Acp5) revealed by doubly deficient mice

To date, two lysosomal acid phosphatases are known to be expressed in cells of the monocyte/phagocyte lineage: the ubiquitously expressed lysosomal acid phosphatase (LAP) and the tartrate-resistant acid phosphatase-type 5 (Acp5). Deficiency of either acid phosphatase results in relatively mild phenotypes, suggesting that these enzymes may be capable of mutual complementation. This prompted us to generate LAP/Acp5 doubly deficient mice. LAP/Acp5 doubly deficient mice are viable and fertile but display marked alterations in soft and mineralised tissues. They are characterised by a progressive hepatosplenomegaly, gait disturbances and exaggerated foreshortening of long bones. Histologically, these animals are distinguished by an excessive lysosomal storage in macrophages of the liver, spleen, bone marrow, kidney and by altered growth plates. Microscopic analyses showed an accumulation of osteopontin adjacent to actively resorbing osteoclasts of Acp5- and LAP/Acp5-deficient mice. In osteoclasts of phosphatase-deficient mice, vacuoles were frequently found which contained fine filamentous material. The vacuoles in Acp5- and LAP/Acp5 doubly-deficient osteoclasts also contained crystallite-like features, as well as osteopontin, suggesting that Acp5 is important for processing of this protein. This is further supported by biochemical analyses that demonstrate strongly reduced dephosphorylation of osteopontin incubated with LAP/Acp5-deficient bone extracts. Fibroblasts derived from LAP/Acp5 deficient embryos were still able to dephosphorylate mannose 6-phosphate residues of endocytosed arylsulfatase A. We conclude that for several substrates LAP and Acp5 can substitute for each other and that these acid phosphatases are essential for processing of non-collagenous proteins, including osteopontin, by osteoclasts.

EEA1, a Tethering Protein of the Early Sorting Endosome, Shows a Polarized Distribution in Hippocampal Neurons, Epithelial Cells, and Fibroblasts

EEA1 is an early endosomal Rab5 effector protein that has been implicated in the docking of incoming endocytic vesicles before fusion with early endosomes. Because of the presence of complex endosomal pathways in polarized and nonpolarized cells, we have examined the distribution of EEA1 in diverse cell types. Ultrastructural analysis demonstrates that EEA1 is present on a subdomain of the early sorting endosome but not on clathrin-coated vesicles, consistent with a role in providing directionality to early endosomal fusion. Furthermore, EEA1 is associated with filamentous material that extends from the cytoplasmic surface of the endosomal domain, which is also consistent with a tethering/docking role for EEA1. In polarized cells (Madin-Darby canine kidney cells and hippocampal neurons), EEA1 is present on a subset of “basolateral-type” endosomal compartments, suggesting that EEA1 regulates specific endocytic pathways. In both epithelial cells and fibroblastic cells, EEA1 and a transfected apical endosomal marker, endotubin, label distinct endosomal populations. Hence, there are at least two distinct sets of early endosomes in polarized and nonpolarized mammalian cells. EEA1 could provide specificity and directionality to fusion events occurring in a subset of these endosomes in polarized and nonpolarized cells.

Ultrastructure of sperm development in the free-living marine nematodes of the family Chromadoridae (Chromadorida: Chromadorina)

Spermatogenesis in two species of free-living marine nematodes from the family Chromadoridae (Panduripharynx pacifica and Euchromadora robusta) was studied electron-microscopically. The spermatogonia of both species are undifferentiated polygonal cells with a large nucleus surrounded by a small amount of cytoplasm. In P. pacifica the cytoplasm of spermatocytes contains many Golgi bodies, cisternae of RER, ribosomes, mitochondria and dense spherical bodies. Filamentous material is accumulated in spermatids, which contain only mitochondria and a fragmented (or lobed) nucleus devoid of the nuclear envelope. The immature sperm resembles the late spermatid: its central filamentous area is surrounded by chromatine particles and occasional mitochondria. The immature sperm plasma membrane forms deep infoldings. Mature spermatozoa from the uterus consist of a small main cell body (MCB) bearing a prominent pseudopod filled with cytoskeleton filaments. The MCB contains a nucleus and mitochondria. Spermatogenesis in E. robusta (studied only in testes) resembles that described for P. pacifica, but spermatocytes of E. robusta show much lower metabolic activity and, as a result, a smaller mass of filamentous material is stored in the spermatids and immature sperm. The spermatozoa of P. pacifica and the immature sperm of E. robusta have the main ultrastructural features characteristic for nematodes (amoeboid nature, absence of axoneme, acrosome and nuclear envelope). No aberrant organelles special for many nematode sperm (membranous organelles, paracrystalline fibrous bodies and their complexes) were found during sperm development of the chromadorids studied. In this respect their spermatogenesis differs significantly from that in secernents and monhysterids.La spermatogenèse a été étudiée en microscopie électronique à transmission chez deux espèces de nématodes libres marins (Panduripharynx pacifica et Euchromadora robusta) de la famille des Chromadoridae. Les spermatogonies, chez les deux espèces, sont des cellules indifférenciées avec un grand noyau entouré d'une petite quantité de cytoplasme. Chez P. pacifica, le cytoplasme des spermatocytes contient de nombreux corps de Golgi, des cisternae du RER, des ribosomes, des mitochondries et des corps sphériques denses. Le matériel filamenteux est accumulé dans les spermatides qui contiennent seulement des mitochondries et un noyau fragmenté (ou lobé) dépourvu d'enveloppe nucléaire. Le sperme immature resemble aux dernières spermatides: son aire centrale filamenteuse est entourée par des particules de chromatine et quelques mitochondries. La membrane plasmatique du sperme immature forme des invaginations profondes. Les spermatozoïdes matures, dans l'utérus, sont constitués par un petit corps cellulaire principal (MCB) portant un pseudopode proéminent rempli de filaments de cytosquelette. Le MCB contient un noyau et des mitochondries. La spermatogenèse chez E. robusta (étudiées seulement au niveau des testicules) ressemble à celle décrite chez P. pacifica, mais les spermatocytes d' E. robusta sont le siège d'une activité métabolique plus faible et, par conséquent, une masse plus faible de matériel filamenteux est stockée dans les spermatides et dans le sperme immature. Les spermatozoïdes de P. pacifica et le sperme immature d' E. robusta ont les mêmes caractéristiques ultrastructurales pour des nématodes (nature amiboïde, absence d'axonème, d'acrosome et d'enveloppe nucléaire) mais aucune des organelles aberrantes particuliéres à de nombreux spermes de nématodes (organelles membraneuses, corps fibreux paracrystallins et leurs complexes) n'ont été identifiées pendant le développement du sperme chez les Chromadorides étudiés. Par cet aspect, leur spermatogenèse diffère significativement de celle des Secernentes et des Monhysterides.