Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China
During the pandemic of COVID-19, Macau faces tremendous pressure because it is a famous gambling and tourism city with the world’s highest population density. The Macau government implemented decisive public health intervention to control the transmission of COVID-19, and there were only two independent outbreaks in Macau. In the second outbreak, all 35 cases were infected in foreign countries. They were quarantined in airborne infection isolation rooms for at least 14 days with reverse transcription-polymerase chain reaction (RT-PCR) tests after hospital discharge. Twelve (34.3%) of them had re-positive SARS-CoV-2 test results, and none of them presented any COVID-19 signs or symptoms during the entire quarantine period. In this study, the re-positive patients were more likely to be diagnosed in the early stage of the disease with a longer hospital stay. Virus re-infection is impossible in this high standard isolation setting, and reactivation is also unlikely, so that residual virus nucleic acid should be the possible reason for this phenomenon. Due to limited data about the risk of re-positive patients, it is better to quarantine patients after discharge for a prolonged period with repeat RT-PCR tests to minimize the community’s potential risk, particularly in the regions with relative plenty of resources and low community infection rate such as Macau.
Wong et al. (2021) Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China. PeerJ 9:e11170 https://doi.org/10.7717/peerj.11170
A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19
Background & Objectives The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. Methods In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. Results Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol), thymoquinone (−4.71 kcal/mol), and andrographolide (Kalmegh) (−4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. Interpretation & Conclusions The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.
Srivastava et al. (2021) A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19. PeerJ 9:e11171 https://doi.org/10.7717/peerj.11171
Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity
This study investigated the effect of co-culturing microalgae with a floc-forming bacterium. Of the six microalgae isolated from a biofloc sample, only Thalassiosira weissflogii, Chlamydomonas sp. and Chlorella vulgaris were propagated successfully in Conway medium. Hence, these species were selected for the experiment comparing microalgae axenic culture and co-culture with the floc-forming bacterium, Bacillus infantis. Results obtained showed that the co-culture had higher microalgae biomass compared to the axenic culture. A similar trend was also observed concerning the lipid content of the microalgae-bacterium co-cultures. The cell number of B. infantis co-cultured with T. weissflogii increased during the exponential stage until the sixth day, but the other microalgae species experienced a significant early reduction in cell density of the bacteria at the exponential stage. This study represents the first attempt at co-culturing microalgae with B. infantis, a floc-forming bacterium, and observed increased biomass growth and lipid accumulation compared to the axenic culture.
Yee et al. (2021) Marine microalgae co-cultured with floc-forming bacterium: Insight into growth and lipid productivity. PeerJ 9:e11217 https://doi.org/10.7717/peerj.11217
Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)
Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.
Bendik et al. (2021) Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum). PeerJ 9:e11246 https://doi.org/10.7717/peerj.11246
Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans
Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Here we compile 211 instances of epifaunal crustaceans recorded on Hydromedusae and Scyphomedusae from a century of literature. These include 78 identified crustacean species in 65 genera across nine orders found upon 37 Hydromedusa species and 48 Scyphomedusae. The crustacean life stage, location, nature of the association with the medusa, years, months, and depths are compiled to form a comprehensive view of the current state of the literature. Additionally, this review highlights areas where the current literature is lacking, particularly noting our poor understanding of the relationships between juvenile crabs of commercially valuable species and medusae.
Muffett et al. (2021) Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans. PeerJ 9:e11281 https://doi.org/10.7717/peerj.11281
Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
Garibian et al. (2021) Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 9:e11310 https://doi.org/10.7717/peerj.11310
Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens
As land use change drives global insect declines, the value of enhancing habitat in urban and suburban landscapes has become increasingly important for flower-visiting insects. In order to help identify best landscaping practices, we conducted plant surveys and insect bowl-trap surveys in 34 suburban yards for 21 months in Gainesville, FL, USA, which resulted in 274 paired days of plant and insect survey data. We assessed the impact of nearest greenspace size, distance to greenspace, yard area, plant richness, plant type, bloom abundance, bloom richness and bloom evenness on insect abundance and richness. Our samples include 34,972 insects captured, 485,827 blooms counted and 774 species of plants recorded. We found that bloom evenness had a modulating effect on bloom abundance—a more even sample of the same number of blooms would have a disproportionately greater positive impact on flower visitor richness, insect richness and insect abundance. Bloom abundance was also highly significant and positively associated with flower visitor abundance, but nearest greenspace size, distance to greenspace, plant type (native vs. non-native vs. Florida Friendly), and yard area were not found to be important factors. Plant richness was a highly significant factor, but its effect size was very small.
Braatz et al. (2021) Bloom evenness modulates the influence of bloom abundance on insect community structure in suburban gardens. PeerJ 9:e11132 https://doi.org/10.7717/peerj.11132
Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of capacity to adapt to rapidly changing environmental conditions.
Price et al. (2021) Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity. PeerJ 9:e10993 https://doi.org/10.7717/peerj.10993
The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon
Echolocation clicks can reflect the anatomy of the vocalizing animal, enabling the distinction of species. River dolphins from the family Iniidae are formally represented by one species and two subspecies (Inia geoffrensis geoffrensis and I. g. humboldtiana). Additionally, two other species have been proposed (I. boliviensis and I. araguaiaensis) regarding its level of restricted distribution and morph-genetics differences. For the Committee on Taxonomy of the Society for Marine Mammalogy, the specific status of the proposed species relies on further knowledge on morphology, ecology, and genetics. Given that species-specific status is required for conservation efforts, we described and compared the echolocation clicks of Inia spp., searching for specific differences on their vocalizations. The sounds were captured with a Cetacean Research ™ C54XRS (+3/−20 dB, −185 dB re: 1V/μPa) in Guaviare River (Orinoco basin), Madeira River (Madeira basin), Xingu River (Amazon Basin), and Araguaia River (Tocantins-Araguaia basin). We found significant differences in all analyzed parameters (peak frequency, 3 dB bandwidth, 10 dB bandwidth and inter-click interval) for all species and subspecies. Differences in acoustical parameters of clicks are mainly related to the animal’s internal morphology, thus this study may potentially support with information for the species-level classification mostly of I. araguaiaensis (the Araguaian boto). Classifying the Araguaian boto separately from I. geoffrensis has important implications for the species in terms of conservation status, since it is restricted to a highly impacted river system.
Melo et al. (2021) The biosonar of the boto: evidence of differences among species of river dolphins (Inia spp.) from the Amazon. PeerJ 9:e11105 https://doi.org/10.7717/peerj.11105
Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage
Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
Thomsen et al. (2021) Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage. PeerJ 9:e11119 https://doi.org/10.7717/peerj.11119