Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding

Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture. Thus, for quality control purposes, an accurate and effective method should be provided for taxonomic identification of Faeces Vespertilionis. In this study, 26 samples of Faeces Vespertilionis from ten provinces in China were tested using DNA metabarcoding. Seven operational taxonomic units (OTUs) were detected as belonging to bats. Among them, Hipposideros armiger (Hodgson, 1835) and Rhinolophus ferrumequinum (Schober and Grimmberger, 1997) were the main host sources of Faeces Vespertilionis samples, with average relative abundances of 59.3% and 24.1%, respectively. Biodiversity analysis showed that Diptera and Lepidoptera were the most frequently consumed insects. At the species level, 19 taxa were clearly identified. Overall, our study used DNA metabarcoding to analyze the biological composition of Faeces Vespertilionis, which provides a new idea for the quality control of this special traditional Chinese medicine.

Geochemical characterization of clastic sediments sheds light on energy sources and on alleged anthropogenic impacts in cave ecosystems

Caves are usually oligotrophic ecosystems, where the organic matter represents a limiting factor to the hypogeal community and sediments are often a significant energy source. With a view to identifying the energy input influencing the ecological processes occurring in caves, as well as the potential alteration sources of the natural equilibriums, geochemical features of several typologies of clastic sediments from the Pertosa-Auletta Cave (Italy) were investigated. The collected sediments, analyzed for a number of chemical (organic matter, Al, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, S, Si, Sr, Ti, V, Zn concentrations) and mineralogical (quartz, calcite, dolomite, clay minerals) characteristics, showed a different composition. Overall, their origin is supposed to be allochthonous, related to the important fluviokarst activities interesting the cave in the past, whereas the abundance of calcitic and dolomitic compounds can be autochthonous, being the carbonate the main host rock. The highest concentrations of organic matter, together with C, Cu, Mo, N, P, Pb, S and Zn, highlighted in one sample composed mainly of bats guano, revealed an important bioavailable energy input as well as a pollutant accumulation, mainly of anthropogenic origin.

Morphological and Phylogenetic Analyses Reveal a New Species of Ceratocystiopsis (Ophiostomataceae, Ophiostomatales) Associated with Ips subelongatus in Inner Mongolia (China) with Weak Host Pathogenicity

Ophiostomatoid fungi are known for their associations with bark beetles, and some species are important sources of tree diseases. Ceratocystiopsis is a genus of the ophiostomatoid fungi in order Ophiostomatales. The shortage of DNA barcodes for many species in this genus has resulted in the presence of many unnamed cryptic species. In this study, Ceratocystiopsis subelongati sp. nov. associated with Ips subelongatus infesting Pinus sylvestris var. mongolica in Inner Mongolia, China, was identified and described based on phylogenetic inference of multi-gene DNA sequences and morphological characteristics. The species is characterized by a hyalorhinocladiella- to sporothrix-like asexual state and an optimal growth temperature of 30 °C. Artificial inoculation tests in the field showed that it is mildly pathogenic to five-year-old larch trees, the main host of I. subelongatus. It is also the first described Ceratocystiopsis species associated with I. subelongatus in China. This discovery should provide new avenues for studying the symbiosis between bark beetles and ophiostomatoid fungi.

Evaluation of Reference Genes in Glenea cantor (Fabricius) by Using qRT-PCR

Kapok is the main host of Glenea cantor (Fabricius), which causes serious damage and is difficult to control. In severe cases, it often causes the kapok trees to die continuously, which seriously affects the results of urban landscaping. To provide reference for the functional research on related genes in G. cantor, we screened the stable expression of candidate reference genes at different developmental stages (i.e., eggs, larvae, pupae, and adults), in various adult tissues (i.e., head, thorax, abdomen, feet, antennae, and wings), and sexes (i.e., male pupae, female pupae, male adults, and female adults). In this study, 12 candidate reference genes (i.e., ACTINLIKE, ACTININ, TUB, RPL36, RPL32, RPS20, TBP, GAPDH, 18S rRNA, EF1A1, EF1A2, and UBQ) were evaluated using different adult tissues, developmental stages, and sexes. RefFinder, geNorm, NormFinder, and BestKeeper were used to evaluate and comprehensively analyze the stability of the expression of the candidate reference genes. The results show that RPL32 and EF1A1 were the most suitable reference genes in the different adult tissues, and RPL36 and EF1A1 were best at the different developmental stages. RPL36 and EF1A2 were the best fit for the qRT-PCR reference genes in the different sexes, while RPL36 and EF1A1 were the most appropriate qRT-PCR reference genes in all samples. Results from geNorm showed that the optimal number of reference genes was two. We also surveyed the expression of cellulase at the different developmental stages and in the different adult tissues. Results further verified the reliability of the reference genes, and confirmed the best reference genes under the different experimental conditions. This study provides a useful tool for molecular biological studies on G. cantor.

Intranasal oxygen reverses hypoxaemia in immobilised free-ranging capybaras (Hydrochoerus hydrochaeris)

Capybara (Hydrochoerus hydrochaeris) is the main host of tick-borne pathogens causing Brazilian spotted fever; therefore, controlling its population is essential, and this may require chemical restraint. We assessed the impact of chemical restraint protocols on the partial pressure of arterial oxygen (PaO2) and other blood variables in 36 capybaras and the effect of different flows of nasal oxygen (O2) supplementation. The capybaras were hand-injected with dexmedetomidine (5 μg/kg) and midazolam (0.1 mg/kg) and butorphanol (0.2 mg/kg) (DMB, n = 18) or methadone (0.1 mg/kg) (DMM, n = 18). One-third of the animals were maintained in ambient air throughout the procedure, and one-third were administered intranasal 2 L/min O2 after 30 min whereas the other third were administered 5 L/min O2. Arterial blood gases, acid-base status, and electrolytes were assessed 30 and 60 min after drug injection. The DMB and DMM groups did not vary based on any of the evaluated variables. All animals developed hypoxaemia (PaO2 44 [30; 73] mmHg, SaO2 81 [62; 93] %) 30 min before O2 supplementation. Intranasal O2 at 2 L/min improved PaO2 (63 [49; 97] mmHg and SaO2 [92 [85; 98] %), but 9 of 12 capybaras remained hypoxaemic. A higher O2 flow of 5 L/min was efficient in treating hypoxaemia (PaO2 188 [146; 414] mmHg, SaO2 100 [99; 100] %) in all the 12 animals that received it. Both drug protocols induced hypoxaemia, which could be treated with intranasal oxygen supplementation.

Habitat Structure, Resources and Natural Enemies: Their Influence on Population Fluctuations of the Kowhai Moth Uresiphita Polygonalis Maorialis (Felder)

<p><b>The importance of habitat structure has been historically discussed in terms of its influence on diversity, distribution and abundance of living organisms. In this regard, the population fluctuations of any particular species, particularly outbreaking insect species, can be expected to be profoundly influenced by the structure of the habitat. A set of ecological hypotheses, such as, the associational resistance, plant decoy, habitat heterogeneity and resource concentration have implicitly included the structure of the habitat determined by the structure (size, density, physical location) of the host plant and other surrounding plant species. Moreover, type, quality and availability of resources, in addition to the presence of other interacting organisms, e.g. competitors, predators and parasites, have also been considered determining factors in the population fluctuation of outbreaking species. The aim of this thesis is to contribute to the understanding of how the outbreaks of the kowhai moth, U. polygonalis maorialis, relate to the physical structure of the habitat, the availability of resources, specific host plants and to natural enemies.</b></p> <p>In the first experimental chapter of my thesis I studied the fluctuations of the U. polygonalis maorialis larvae and their impacts on the defoliation levels of Sophora spp. plants. I carried out a survey in urban and suburban areas of Wellington city. I examined levels of defoliation of the host plants and population fluctuations in terms of a set of biotic and abiotic variables. These variables were selected in order to cover a range of measures of habitat structure, resource availability and invertebrate community. I modelled such responses to find which variables better explained the observed defoliation and larval population fluctuations. The best fitted model showed that levels of observed defoliation were explained by the structure of the vegetation surrounding the main host plant (vertical and horizontal) and the species of host plant. Population fluctuations of the kowhai moth were explained by the following predicting variables: density of natural enemies, structure of the vegetation surrounding the main host plant (vertical and horizontal), host plant size, level of habitat disturbance, type of habitat (urban/suburban) and the Sophora spp.</p> <p>In my second experimental chapter, I focused on the importance of availability of resources to explain observed densities of U. polygonalis maorialis and phytophagous insects. In my observational experiment I tested the resource concentration hypothesis and the natural enemies hypothesis, by studying the fluctuations of U. polygonalis maorialis larvae on individuals of Sophora microphylla plants located in gardens across Wellington city. Larval densities were found to be higher on smaller plants than large plants, whereas natural enemies did not show specific responses to plant size. In my manipulative experiment I originally aimed for the establishment of U. polygonalis maorialis in the experimental plots. Unfortunately, these were not colonised by U. polygonalis maorialis, instead I studied phytophagous insects that colonised the plots. I found no differences among the S. microphylla treatments for the levels of establishment of phytophagous invertebrates. On the contrary, the amount of nil records was high and there was an overall high variability among treatments and low rate of establishment throughout the sampling season. Nevertheless, natural enemies were found to occur more often at higher densities in plots with lower plant density in only two specific dates.</p> <p>Uresiphita polygonalis maorialis is the main defoliator of Sophora spp in New Zealand. In this context I studied the feeding and oviposition preferences of the moth for the three most commonly found species of Sophora plants in Wellington city. Sophora tetraptera was the preferred species chosen by the female moth. The same species was also the most palatable and preferred when confronted to S. microphylla and S. prostrata. These patterns observed in controlled conditions are coincident with observations made in the field throughout the study.</p> <p>Within the set of variables determined by the invertebrate community, the influence of natural enemies on an herbivorous population is one of the most important in terms of population regulation. In my last experimental chapter I found a positive correlation among the parasitism by M. pulchricornis and U. polygonalis maorialis larval densities, which opens the possibilities for future research to explore the potential existence of population regulation mechanisms between these two taxa.</p> <p>Overall, the results of my thesis highlight the importance of understanding the influence of the structure of the habitat, types of resources provided by plants and natural enemies in determining the fluctuations of outbreaking insect species.</p>

Habitat Structure, Resources and Natural Enemies: Their Influence on Population Fluctuations of the Kowhai Moth Uresiphita Polygonalis Maorialis (Felder)

<p><b>The importance of habitat structure has been historically discussed in terms of its influence on diversity, distribution and abundance of living organisms. In this regard, the population fluctuations of any particular species, particularly outbreaking insect species, can be expected to be profoundly influenced by the structure of the habitat. A set of ecological hypotheses, such as, the associational resistance, plant decoy, habitat heterogeneity and resource concentration have implicitly included the structure of the habitat determined by the structure (size, density, physical location) of the host plant and other surrounding plant species. Moreover, type, quality and availability of resources, in addition to the presence of other interacting organisms, e.g. competitors, predators and parasites, have also been considered determining factors in the population fluctuation of outbreaking species. The aim of this thesis is to contribute to the understanding of how the outbreaks of the kowhai moth, U. polygonalis maorialis, relate to the physical structure of the habitat, the availability of resources, specific host plants and to natural enemies.</b></p> <p>In the first experimental chapter of my thesis I studied the fluctuations of the U. polygonalis maorialis larvae and their impacts on the defoliation levels of Sophora spp. plants. I carried out a survey in urban and suburban areas of Wellington city. I examined levels of defoliation of the host plants and population fluctuations in terms of a set of biotic and abiotic variables. These variables were selected in order to cover a range of measures of habitat structure, resource availability and invertebrate community. I modelled such responses to find which variables better explained the observed defoliation and larval population fluctuations. The best fitted model showed that levels of observed defoliation were explained by the structure of the vegetation surrounding the main host plant (vertical and horizontal) and the species of host plant. Population fluctuations of the kowhai moth were explained by the following predicting variables: density of natural enemies, structure of the vegetation surrounding the main host plant (vertical and horizontal), host plant size, level of habitat disturbance, type of habitat (urban/suburban) and the Sophora spp.</p> <p>In my second experimental chapter, I focused on the importance of availability of resources to explain observed densities of U. polygonalis maorialis and phytophagous insects. In my observational experiment I tested the resource concentration hypothesis and the natural enemies hypothesis, by studying the fluctuations of U. polygonalis maorialis larvae on individuals of Sophora microphylla plants located in gardens across Wellington city. Larval densities were found to be higher on smaller plants than large plants, whereas natural enemies did not show specific responses to plant size. In my manipulative experiment I originally aimed for the establishment of U. polygonalis maorialis in the experimental plots. Unfortunately, these were not colonised by U. polygonalis maorialis, instead I studied phytophagous insects that colonised the plots. I found no differences among the S. microphylla treatments for the levels of establishment of phytophagous invertebrates. On the contrary, the amount of nil records was high and there was an overall high variability among treatments and low rate of establishment throughout the sampling season. Nevertheless, natural enemies were found to occur more often at higher densities in plots with lower plant density in only two specific dates.</p> <p>Uresiphita polygonalis maorialis is the main defoliator of Sophora spp in New Zealand. In this context I studied the feeding and oviposition preferences of the moth for the three most commonly found species of Sophora plants in Wellington city. Sophora tetraptera was the preferred species chosen by the female moth. The same species was also the most palatable and preferred when confronted to S. microphylla and S. prostrata. These patterns observed in controlled conditions are coincident with observations made in the field throughout the study.</p> <p>Within the set of variables determined by the invertebrate community, the influence of natural enemies on an herbivorous population is one of the most important in terms of population regulation. In my last experimental chapter I found a positive correlation among the parasitism by M. pulchricornis and U. polygonalis maorialis larval densities, which opens the possibilities for future research to explore the potential existence of population regulation mechanisms between these two taxa.</p> <p>Overall, the results of my thesis highlight the importance of understanding the influence of the structure of the habitat, types of resources provided by plants and natural enemies in determining the fluctuations of outbreaking insect species.</p>

Leprosy in wild chimpanzees

Humans are considered as the main host for Mycobacterium leprae1, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates4–7, the exact origins of infection remain unclear. Here we describe leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in Cantanhez National Park, Guinea-Bissau and Taï National Park, Côte d’Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence of M. leprae as the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). These findings suggest that M. leprae may be circulating in more wild animals than suspected, either as a result of exposure to humans or other unknown environmental sources.

SDAV, the Rat Coronavirus—How Much Do We Know about It in the Light of Potential Zoonoses

Sialodacryoadenitis virus (SDAV) is known to be an etiological agent, causing infections in laboratory rats. Until now, its role has only been considered in studies on respiratory and salivary gland infections. The scant literature data, consisting mainly of papers from the last century, do not sufficiently address the topic of SDAV infections. The ongoing pandemic has demonstrated, once again, the role of the Coronaviridae family as extremely dangerous etiological agents of human zoonoses. The ability of coronaviruses to cross the species barrier and change to hosts commonly found in close proximity to humans highlights the need to characterize SDAV infections. The main host of the infection is the rat, as mentioned above. Rats inhabit large urban agglomerations, carrying a vast epidemic threat. Of the 2277 existing rodent species, 217 are reservoirs for 66 zoonotic diseases caused by viruses, bacteria, fungi, and protozoa. This review provides insight into the current state of knowledge of SDAV characteristics and its likely zoonotic potential.

TR Locus Annotation and Characteristics of Rhinolophus ferrumequinum

T-cell antigen receptors (TRs) in vertebrates can be divided into αβ or γδ, encoded by TRA/D, TRG, or TRB loci. TRs play a central role in mammal cellular immunity, which occurs by rearrangement of V, D, J, and C genes in the loci. The bat is the only mammal with flying ability and is considered the main host of zoonotic viruses, an important public health concern. However, at present, little is known about the composition of bat TR genes. Based on the whole genome sequence of the greater horseshoe bat (Rhinolophus ferrumequinum) and referring to the TR/IG annotation rules formulated by the international ImMunoGeneTics information system (IMGT), we present a complete annotation of TRA/D, TRG, and TRB loci of R. ferrumequinum. A total of 128 V segments, three D segments, 85 J segments, and 6 C segments were annotated and compared with other known mammalian data. The characteristics of the TR locus and germline genes of R. ferrumequinum are analyzed.