Direct-print three-dimensional electrodes for large- scale, high-density, and customizable neural inter- faces.

Silicon-based planar microelectronics is a powerful tool for scalably recording and modulating neural activity at high spatiotemporal resolution, but it remains challenging to target neural structures in three dimensions (3D). We present a method for directly fabricating 3D arrays of tissue-penetrating microelectrodes onto silicon microelectronics. Leveraging a high-resolution 3D printing technology based on 2-photon polymerization and scalable microfabrication processes, we fabricated arrays of 6,600 microelectrodes 10-130 µm tall and at 35-µm pitch onto a planar silicon-based microelectrode array. The process enables customizable electrode shape, height and positioning for precise targeting of neuron populations distributed in 3D. As a proof of concept, we addressed the challenge of specifically targeting retinal ganglion cell (RGC) somas when interfacing with the retina. The array was customized for insertion into the retina and recording from somas while avoiding the axon layer. We verified locations of the microelectrodes with confocal microscopy and recorded high-resolution spontaneous RGC activity at cellular resolution. This revealed strong somatic and dendritic components with little axon contribution, unlike recordings with planar microelectrode arrays. The technology could be a versatile solution for interfacing silicon microelectronics with neural structures and modulating neural activity at large scale with single-cell resolution.

Evaluating species in Botryosphaeriales.

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods. Citation: Zhang W, Groenewald JZ, Lombard L, et al. 2021. Evaluating species in Botryosphaeriales. Persoonia 46: 63-115. https://doi.org/10.3767/persoonia.2021.46.03.

Decreased sensitivity of the circadian system to light in current, but not remitted depression.

BACKGROUND: Misalignment of circadian timing in patients with depression has commonly been reported, but the underlying mechanisms are not known. Individual differences in the sensitivity of the circadian system to light affect how the biological clock synchronizes with the external environment and can lead to misalignment of rhythms. We investigated the sensitivity of the circadian system to light in unmedicated (for >3 months) women with a current or previous diagnosis of major depression, and healthy controls. METHODS: Baseline melatonin levels in dim light (<1 lux) were assessed, followed by melatonin levels in normal indoor lighting of 100 lux in order to determine melatonin suppression. RESULTS: Patients currently experiencing a depressive episode showed significantly lower levels of melatonin suppression to light compared to remitted patients and controls, with large effect sizes. Remitted patients and controls showed similar suppression. LIMITATIONS: The relatively small sample, and lack of long-term, within subject assessments, make it difficult to determine the potential causal role of reduced light sensitivity in the development of circadian disruption. CONCLUSIONS: We conclude that hyposensitivity of the circadian system to light may contribute to circadian misalignment in patients with depression. Interventions that increase sensitivity to light or provide stronger light cues may assist in normalizing circadian clock function.

Phylogenetic revision of Camarosporium (Pleosporineae, Dothideomycetes) and allied genera.

A concatenated dataset of LSU, SSU, ITS and tef1 DNA sequence data was analysed to investigate the taxonomic position and phylogenetic relationships of the genus Camarosporium in Pleosporineae (Dothideomycetes). Newly generated sequences from camarosporium-like taxa collected from Europe (Italy) and Russia form a well-supported monophyletic clade within Pleosporineae. A new genus Camarosporidiella and a new family Camarosporidiellaceae are established to accommodate these taxa. Four new species, Neocamarosporium korfii, N. lamiacearum, N. salicorniicola and N. salsolae, constitute a strongly supported clade with several known taxa for which the new family, Neocamarosporiaceae, is introduced. The genus Staurosphaeria based on S. lycii is resurrected and epitypified, and shown to accommodate the recently introduced genus Hazslinszkyomyces in Coniothyriaceae with significant statistical support. Camarosporium quaternatum, the type species of Camarosporium and Camarosporomyces flavigena cluster together in a monophyletic clade with significant statistical support and sister to the Leptosphaeriaceae. To better resolve interfamilial/intergeneric level relationships and improve taxonomic understanding within Pleosporineae, we validate Camarosporiaceae to accommodate Camarosporium and Camarosporomyces. The latter taxa along with other species are described in this study.

Families of Diaporthales based on morphological and phylogenetic evidence.

Diaporthales is an important ascomycetous order comprising phytopathogenic, saprobic, and endophytic fungi, but interfamilial taxonomic relationships are still ambiguous. Despite its cosmopolitan distribution and high diversity with distinctive morphologies, this order has received relativelyiaceae, Macrohilaceae, Melanconidaceae, Pseudoplagiostomaceae, Schizoparmaceae, Stilbosporaceae and Sydowiellaceae. Taxonomic uncertainties among genera are also clarified and recurrent discrepancies in the taxonomic position of families within the Diaporthales are discussed. An updated outline and key to families and genera of the order is presented.

A multiproxy approach to evaluate biocidal treatments on biodeteriorated majolica glazed tiles.

The Fishing House located on the grounds of the Marquis of Pombal Palace, Oeiras, Portugal, was built in the 18th century. During this epoch, Portuguese gardens, such as the one surrounding the Fishing House, were commonly ornamented with glazed wall tile claddings. Currently, some of these outdoor tile panels are covered with dark colored biofilms, contributing to undesirable aesthetic changes and eventually inducing chemical and physical damage to the tile surfaces. Phylogenetic analyses revealed that the investigated biofilms are mainly composed of green algae, cyanobacteria and dematiaceous fungi. With the aim of mitigating biodeterioration, four different biocides (TiO2 nanoparticles, Biotin® T, Preventol® RI 80 and Albilex Biostat® ) were applied in situ to the glazed wall tiles. Their efficacy was monitored by visual examination, epifluorescence microscopy and DNA-based analysis. Significant changes in the microbial community composition were observed 4 months after treatment with Preventol® RI 80 and Biotin® T. Although the original community was inactivated after these treatments, an early stage of re-colonization was detected 6 months after the biocide application. TiO2 nanoparticles showed promising results due to their self-cleaning effect, causing the detachment of the biofilm from the tile surface, which remained clean 6 and even 24 months after biocide application. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers.

AIMS: Potting media and organic fertilizers (OFs) are commonly used in agricultural systems. However, there is a lack of studies on the efficiency of culture-based techniques in assessing the level of fungal diversity in these products. A study was conducted to investigate the efficiency of seven culture-based techniques and pyrosequencing for characterizing fungal diversity in potting media and OFs. METHODS AND RESULTS: Fungal diversity was evaluated using serial dilution, direct plating and baiting with carrot slices, potato slices, radish seeds, cucumber seeds and cucumber cotyledons. Identity of all the isolates was confirmed on the basis of the internal transcribed spacer region of the ribosomal RNA (ITS rRNA) sequence data. The direct plating technique was found to be superior over other culture-based techniques in the number of fungal species detected. It was also found to be simple and the least time consuming technique. Comparing the efficiency of direct plating with 454 pyrosequencing revealed that pyrosequencing detected 12 and 15 times more fungal species from potting media and OFs respectively. Analysis revealed that there were differences between potting media and OFs in the dominant phyla, classes, orders, families, genera and species detected. Zygomycota (52%) and Chytridiomycota (60%) were the predominant phyla in potting media and OFs respectively. CONCLUSIONS: The superiority of pyrosequencing over cultural methods could be related to the ability to detect obligate fungi, slow growing fungi and fungi that exist at low population densities. SIGNIFICANCE AND IMPACT OF THE STUDY: The evaluated methods in this study, especially direct plating and pyrosequencing, may be used as tools to help detect and reduce movement of unwanted fungi between countries and regions.

A phylogenetic study of Dothiorella and Spencermartinsia species associated with woody plants in Iran, New Zealand, Portugal and Spain.

Dothiorella and Spencermartinsia are two botryosphaeriaceous genera with dark 2-celled conidia and found in parasitic, saprophytic or endophytic association with various woody host plants. Based on ITS and EF1-α sequence data and morphology, eight new species are described from Iran, New Zealand, Portugal and Spain. Of these, five species are placed in Dothiorella, namely D. iranica, D. parva, D. prunicola, D. sempervirentis and D. striata, and three species belong to Spencermartinsia named as S. citricola, S. mangiferae and S. plurivora. An identification key to the species of each genus is provided.

Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework.

The order Botryosphaeriales represents several ecologically diverse fungal families that are commonly isolated as endophytes or pathogens from various woody hosts. The taxonomy of members of this order has been strongly influenced by sequence-based phylogenetics, and the abandonment of dual nomenclature. In this study, the phylogenetic relationships of the genera known from culture are evaluated based on DNA sequence data for six loci (SSU, LSU, ITS, EF1, BT, mtSSU). The results make it possible to recognise a total of six families. Other than the Botryosphaeriaceae (17 genera), Phyllostictaceae (Phyllosticta) and Planistromellaceae (Kellermania), newly introduced families include Aplosporellaceae (Aplosporella and Bagnisiella), Melanopsaceae (Melanops), and Saccharataceae (Saccharata). Furthermore, the evolution of morphological characters in the Botryosphaeriaceae were investigated via analysis of phylogeny-trait association. None of the traits presented a significant phylogenetic signal, suggesting that conidial and ascospore pigmentation, septation and appendages evolved more than once in the family. Molecular clock dating on radiations within the Botryosphaeriales based on estimated mutation rates of the rDNA SSU locus, suggests that the order originated in the Cretaceous period around 103 (45-188) mya, with most of the diversification in the Tertiary period. This coincides with important periods of radiation and spread of the main group of plants that these fungi infect, namely woody Angiosperms. The resulting host-associations and distribution could have influenced the diversification of these fungi. TAXONOMIC NOVELTIES: New families - Aplosporellaceae Slippers, Boissin & Crous, Melanopsaceae Phillips, Slippers, Boissin & Crous, Saccharataceae Slippers, Boissin & Crous.

The Botryosphaeriaceae: genera and species known from culture.

In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-α and ß-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-α) for the species in each genus. TAXONOMIC NOVELTIES: New species - Neofusicoccum batangarum Begoude, Jol. Roux & Slippers. New combinations - Botryosphaeria fabicerciana (S.F. Chen, D. Pavlic, M.J. Wingf. & X.D. Zhou) A.J.L. Phillips & A. Alves, Botryosphaeria ramosa (Pavlic, T.I. Burgess, M.J. Wingf.) A.J.L. Phillips & A. Alves, Cophinforma atrovirens (Mehl & Slippers) A. Alves & A.J.L. Phillips, Cophinforma mamane (D.E. Gardner) A.J.L. Phillips & A. Alves, Dothiorella pretoriensis (Jami, Gryzenh., Slippers & M.J. Wingf.) Abdollahz. & A.J.L. Phillips, Dothiorella thailandica (D.Q. Dai., J.K. Liu & K.D. Hyde) Abdollahz., A.J.L. Phillips & A. Alves, Dothiorella uruguayensis (C.A. Pérez, Blanchette, Slippers & M.J. Wingf.) Abdollahz. & A.J.L. Phillips, Lasiodiplodia lignicola (Ariyawansa, J.K. Liu & K.D. Hyde) A.J.L. Phillips, A. Alves & Abdollahz., Neoscytalidium hyalinum (C.K. Campb. & J.L. Mulder) A.J.L. Phillips, Groenewald & Crous, Sphaeropsis citrigena (A.J.L. Phillips, P.R. Johnst. & Pennycook) A.J.L. Phillips & A. Alves, Sphaeropsis eucalypticola (Doilom, J.K. Liu, & K.D. Hyde) A.J.L. Phillips, Sphaeropsis porosa (Van Niekerk & Crous) A.J.L. Phillips & A. Alves. Epitypification (basionym) - Sphaeria sapinea Fries. Neotypifications (basionyms) - Botryodiplodia theobromae Pat., Physalospora agaves Henn, Sphaeria atrovirens var. visci Alb. & Schwein.

Mammalian rest/activity patterns explained by physiologically based modeling.

Circadian rhythms are fundamental to life. In mammals, these rhythms are generated by pacemaker neurons in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN is remarkably consistent in structure and function between species, yet mammalian rest/activity patterns are extremely diverse, including diurnal, nocturnal, and crepuscular behaviors. Two mechanisms have been proposed to account for this diversity: (i) modulation of SCN output by downstream nuclei, and (ii) direct effects of light on activity. These two mechanisms are difficult to disentangle experimentally and their respective roles remain unknown. To address this, we developed a computational model to simulate the two mechanisms and their influence on temporal niche. In our model, SCN output is relayed via the subparaventricular zone (SPZ) to the dorsomedial hypothalamus (DMH), and thence to ventrolateral preoptic nuclei (VLPO) and lateral hypothalamus (LHA). Using this model, we generated rich phenotypes that closely resemble experimental data. Modulation of SCN output at the SPZ was found to generate a full spectrum of diurnal-to-nocturnal phenotypes. Intriguingly, we also uncovered a novel mechanism for crepuscular behavior: if DMH/VLPO and DMH/LHA projections act cooperatively, daily activity is unimodal, but if they act competitively, activity can become bimodal. In addition, we successfully reproduced diurnal/nocturnal switching in the rodent Octodon degu using coordinated inversions in both masking and circadian modulation. Finally, the model correctly predicted the SCN lesion phenotype in squirrel monkeys: loss of circadian rhythmicity and emergence of ∼4-h sleep/wake cycles. In capturing these diverse phenotypes, the model provides a powerful new framework for understanding rest/activity patterns and relating them to underlying physiology. Given the ubiquitous effects of temporal organization on all aspects of animal behavior and physiology, this study sheds light on the physiological changes required to orchestrate adaptation to various temporal niches.

Arousal state feedback as a potential physiological generator of the ultradian REM/NREM sleep cycle.

Human sleep episodes are characterized by an approximately 90-min ultradian oscillation between rapid eye movement (REM) and non-REM (NREM) sleep stages. The source of this oscillation is not known. Pacemaker mechanisms for this rhythm have been proposed, such as a reciprocal interaction network, but these fail to account for documented homeostatic regulation of both sleep stages. Here, two candidate mechanisms are investigated using a simple model that has stable states corresponding to Wake, REM sleep, and NREM sleep. Unlike other models of the ultradian rhythm, this model of sleep dynamics does not include an ultradian pacemaker, nor does it invoke a hypothetical homeostatic process that exists purely to drive ultradian rhythms. Instead, only two inputs are included: the homeostatic drive for Sleep and the circadian drive for Wake. These two inputs have been the basis for the most influential Sleep/Wake models, but have not previously been identified as possible ultradian rhythm generators. Using the model, realistic ultradian rhythms are generated by arousal state feedback to either the homeostatic or circadian drive. For the proposed 'homeostatic mechanism', homeostatic pressure increases in Wake and REM sleep, and decreases in NREM sleep. For the proposed 'circadian mechanism', the circadian drive is up-regulated in Wake and REM sleep, and is down-regulated in NREM sleep. The two mechanisms are complementary in the features they capture. The homeostatic mechanism reproduces experimentally observed rebounds in NREM sleep duration and intensity following total sleep deprivation, and rebounds in both NREM sleep intensity and REM sleep duration following selective REM sleep deprivation. The circadian mechanism does not reproduce sleep state rebounds, but more accurately reproduces the temporal patterns observed in a normal night of sleep. These findings have important implications in terms of sleep physiology and they provide a parsimonious explanation for the observed ultradian rhythm of REM/NREM sleep.

Plectosphaerella species associated with root and collar rots of horticultural crops in southern Italy.

Plectosphaerella cucumerina, most frequently encountered in its Plectosporium state, is well known as a pathogen of several plant species causing fruit, root and collar rot, and collapse. It is considered to pose a serious threat to melon (Cucumis melo) production in Italy. In the present study, an intensive sampling of diseased cucurbits as well as tomato and bell pepper was done and the fungal pathogens present on them were isolated. Phylogenetic relationships of the isolates were determined through a study of ribosomal RNA gene sequences (ITS cluster and D1/D2 domain of the 28S rRNA gene). Combining morphological, culture and molecular data, six species were distinguished. One of these (Pa. cucumerina) is already known. Four new species are described as Plectosphaerella citrullae, Pa. pauciseptata, Pa. plurivora and Pa. ramiseptata. Acremonium cucurbitacearum is shown to be a synonym of Nodulisporium melonis and is transferred to Plectosphaerella as Plectosphaerella melonis comb. nov. A further three known species of Plectosporium are recombined in Plectosphaerella.

Physiologically based quantitative modeling of unihemispheric sleep.

Unihemispheric sleep has been observed in numerous species, including birds and aquatic mammals. While knowledge of its functional role has been improved in recent years, the physiological mechanisms that generate this behavior remain poorly understood. Here, unihemispheric sleep is simulated using a physiologically based quantitative model of the mammalian ascending arousal system. The model includes mutual inhibition between wake-promoting monoaminergic nuclei (MA) and sleep-promoting ventrolateral preoptic nuclei (VLPO), driven by circadian and homeostatic drives as well as cholinergic and orexinergic input to MA. The model is extended here to incorporate two distinct hemispheres and their interconnections. It is postulated that inhibitory connections between VLPO nuclei in opposite hemispheres are responsible for unihemispheric sleep, and it is shown that contralateral inhibitory connections promote unihemispheric sleep while ipsilateral inhibitory connections promote bihemispheric sleep. The frequency of alternating unihemispheric sleep bouts is chiefly determined by sleep homeostasis and its corresponding time constant. It is shown that the model reproduces dolphin sleep, and that the sleep regimes of humans, cetaceans, and fur seals, the latter both terrestrially and in a marine environment, require only modest changes in contralateral connection strength and homeostatic time constant. It is further demonstrated that fur seals can potentially switch between their terrestrial bihemispheric and aquatic unihemispheric sleep patterns by varying just the contralateral connection strength. These results provide experimentally testable predictions regarding the differences between species that sleep bihemispherically and unihemispherically.

Resolving the Diplodia complex on apple and other Rosaceae hosts.

Diplodia species are known as pathogens on many woody hosts, including fruit trees, worldwide. In this study a collection of Diplodia isolates obtained mostly from apple and other Rosaceae hosts were identified based on morphological characters and DNA sequence data from ITS and EF1-α loci. The results show that the diversity of species associated with twig and branch cankers and fruit rot of apples is larger than previously recognised. Four species were identified, namely D. seriata and D. malorum (which is here reinstated for isolates with D. mutila-like conidia). Diplodia intermedia sp. nov. is closely related to D. seriata, and D. bulgarica sp. nov. is morphologically and phylogenetically distinct from all Diplodia species reported from apples.

Fungal Planet description sheets: 128-153.

Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliae-fistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided.

Quantitative modelling of sleep dynamics.

Arousal is largely controlled by the ascending arousal system of the hypothalamus and brainstem, which projects to the corticothalamic system responsible for electroencephalographic (EEG) signatures of sleep. Quantitative physiologically based modelling of brainstem dynamics theory is described here, using realistic parameters, and links to EEG are outlined. Verification against a wide range of experimental data is described, including arousal dynamics under normal conditions, sleep deprivation, stimuli, stimulants and jetlag, plus key features of wake and sleep EEGs.