HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets.

PREMISE: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS: We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS: All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION: HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.

Model for Mitigation of Workplace Transmission of COVID-19 Through Population-Based Testing and Surveillance.

The coronavirus disease-2019 (COVID-19) pandemic is having a widespread impact on societies across the globe. As part of the effort to control transmission in the United States, many businesses either closed or instituted nonpharmaceutical control measures and allowed only essential workers on-site. During summer and fall of 2020, employers began formulating "return to work" strategies designed to mitigate the risk of transmission among employees. On a population level, several countries implemented national testing and surveillance strategies that proved effective in mitigating citizen-to-citizen transmission and contributed to suppressing COVID-19. A crucial component of many such strategies is population-based testing to identify and engage individuals with asymptomatic or presymptomatic infection, which also is relevant to return-to-work strategies. The authors describe an approach that multisite employers might use to help mitigate transmission of COVID-19 in the workplace. This approach leverages a bioinformatics platform informed by real-time PCR test data at the county and subcounty (eg, Public Use Microdata Area) level, allowing for population-based testing to be selectively targeted for employees in geographies with elevated SARS-CoV-2 positivity. A "Command Center" application integrates data from multiple sources (eg, local infection trends, employee symptom diaries, Bluetooth thermometers) in real time, which can be used to inform decisions regarding surveillance and employee self-isolation or quarantine; a mobile phone-based application provides for rapid, secure communication with employees. This overview is based on peer-reviewed literature and the early experience of a large employer with implementing bioinformatics tools to mitigate the impact of the pandemic on the workplace.

Potential effects of climate change on members of the Palaeotropical pitcher plant family Nepenthaceae.

Anthropogenic climate change is predicted to have profound effects on species distributions over the coming decades. In this paper, we used maximum entropy modelling (Maxent) to estimate the effects of projected changes in climate on extent of climatically-suitable habitat for two Nepenthes pitcher plant species in Borneo. The model results predicted an increase in area of climatically-suitable habitat for the lowland species Nepenthes rafflesiana by 2100; in contrast, the highland species Nepenthes tentaculata was predicted to undergo significant loss of climatically-suitable habitat over the same period. Based on the results of the models, we recommend that research be undertaken into practical mitigation strategies, as approximately two-thirds of Nepenthes are restricted to montane habitats. Highland species with narrow elevational ranges will be at particularly high risk, and investigation into possible mitigation strategies should be focused on them.

Nepenthes ampullaria (Nepenthaceae) Pitchers Are Unattractive to Gravid Aedes aegypti and Aedes albopictus (Diptera: Culicidae).

Nepenthes pitcher plants are colonized by a variety of specialized arthropods. As Aedes mosquitoes are container breeders, Nepenthes pitchers are a potential candidate oviposition site for vector species, such as Aedes aegypti (L.) and Aedes albopictus (Skuse). However, Aedes spp. are not commonly encountered in Nepenthes pitchers, and the environment inside the pitchers of some species is lethal to them. One exception is Nepenthes ampullaria Jack, whose pitchers are known to be colonized by Ae. albopictus on very rare occasions. Given that Ae. albopictus larvae can survive in N. ampullaria pitcher fluids, we sought to determine why pitcher colonization is rare, testing the hypothesis that gravid Aedes mosquitoes are deterred from ovipositing into container habitats that have similar characteristics to N. ampullaria pitchers. Using plastic ovitraps of different sizes, colors, and with different types of fluids (based on the characteristics of N. ampullaria pitchers), we compared oviposition rates by Aedes mosquitoes in urban and rural areas within the geographical range of N. ampullaria near Kuala Lumpur, Malaysia. Ovitraps that were black and large (>250-ml capacity) accumulated significantly more eggs than ovitraps that were smaller, or green in color. In terms of size and color, small, green ovitraps are analogous to N. ampullaria pitchers, indicating that these pitchers are not particularly attractive to gravid Ae. albopictus. Although Aedes spp. are capable of colonizing N. ampullaria pitchers, the pitchers are relatively unattractive to gravid females and do not represent a significant habitat for larvae of dengue vectors at present.

Characterization of Shiga Toxigenic Escherichia coli O157 and Non-O157 Isolates from Ruminant Feces in Malaysia.

Shiga toxigenic Escherichia coli (STEC) O157 and several other serogroups of non-O157 STEC are causative agents of severe disease in humans world-wide. The present study was conducted to characterize STEC O157 and non-O157 serogroups O26, O103, O111, O121, O45, and O145 in ruminants in Malaysia. A total of 136 ruminant feces samples were collected from 6 different farms in Peninsular Malaysia. Immunomagnetic beads were used to isolate E. coli O157 and non-O157 serogroups, while PCR was used for the detection and subtyping of STEC isolates. STEC O157:H7 was isolated from 6 (4%) feces samples and all isolates obtained carried stx 2c, eaeA-γ1, and ehxA. Non-O157 STEC was isolated from 2 (1.5%) feces samples with one isolate carrying stx 1a, stx 2a, stx 2c, and ehxA and the other carrying stx 1a alone. The presence of STEC O157 and non-O157 in a small percentage of ruminants in this study together with their virulence characteristics suggests that they may have limited impact on public health.

Bacterial communities associated with the pitcher fluids of three Nepenthes (Nepenthaceae) pitcher plant species growing in the wild.

Nepenthes pitcher plants produce modified jug-shaped leaves to attract, trap and digest insect prey. We used 16S rDNA cloning and sequencing to compare bacterial communities in pitcher fluids of each of three species, namely Nepenthes ampullaria, Nepenthes gracilis and Nepenthes mirabilis, growing in the wild. In contrast to previous greenhouse-based studies, we found that both opened and unopened pitchers harbored bacterial DNA. Pitchers of N. mirabilis had higher bacterial diversity as compared to other Nepenthes species. The composition of the bacterial communities could be different between pitcher types for N. mirabilis (ANOSIM: R = 0.340, p < 0.05). Other Nepenthes species had similar bacterial composition between pitcher types. SIMPER showed that more than 50 % of the bacterial taxa identified from the open pitchers of N. mirabilis were not found in other groups. Our study suggests that bacteria in N. mirabilis are divided into native and nonnative groups.

Interspecific variation in prey capture behavior by co-occurring Nepenthes pitcher plants: evidence for resource partitioning or sampling-scheme artifacts?

Pitcher plants of the genus Nepenthes capture a wide range of arthropod prey for nutritional benefit, using complex combinations of visual and olfactory signals and gravity-driven pitfall trapping mechanisms. In many localities throughout Southeast Asia, several Nepenthes different species occur in mixed populations. Often, the species present at any given location have strongly divergent trap structures and preliminary surveys indicate that different species trap different combinations of arthropod prey, even when growing at the same locality. On this basis, it has been proposed that co-existing Nepenthes species may be engaged in niche segregation with regards to arthropod prey, avoiding direct competition with congeners by deploying traps that have modifications that enable them to target specific prey types. We examined prey capture among 3 multi-species Nepenthes populations in Borneo, finding that co-existing Nepenthes species do capture different combinations of prey, but that significant interspecific variations in arthropod prey combinations can often be detected only at sub-ordinal taxonomic ranks. In all lowland Nepenthes species examined, the dominant prey taxon is Formicidae, but montane Nepenthes trap few (or no) ants and 2 of the 3 species studied have evolved to target alternative sources of nutrition, such as tree shrew feces. Using similarity and null model analyses, we detected evidence for niche segregation with regards to formicid prey among 5 lowland, sympatric Nepenthes species in Sarawak. However, we were unable to determine whether these results provide support for the niche segregation hypothesis, or whether they simply reflect unquantified variation in heterogeneous habitats and/or ant communities in the study sites. These findings are used to propose improvements to the design of field experiments that seek to test hypotheses about targeted prey capture patterns in Nepenthes.

Treatment and biotransformation of highly polluted agro-industrial wastewater from a palm oil mill into vermicompost using earthworms.

In this laboratory-scale study, earthworms were introduced as biodegraders of palm oil mill effluent (POME), which is a wastewater produced from the wet process of palm oil milling. POME was absorbed into amendments (soil or rice straw) in different ratios as feedstocks for the earthworm, Eudrilus eugeniae. The presence of earthworms led to significant increases in pH, electrical conductivity, and nutrient content but decreases in the C/N ratio (0.687-75.8%), soluble chemical oxygen demand (19.7-87.9%), and volatile solids (0.687-52.7%). However, earthworm growth was reduced in all treatments by the end of the treatment process. Rice straw was a better amendment/absorbent relative to soil, with a higher nutrient content and greater reduction in soluble chemical oxygen demand with a lower C/N ratio in the vermicompost. Among all treatments investigated, the treatment with 1 part rice straw and 3 parts POME (w/v) (RS1:3) produced the best quality vermicompost with high nutritional status.

Capture mechanism in Palaeotropical pitcher plants (Nepenthaceae) is constrained by climate.

BACKGROUND AND AIMS: Nepenthes (Nepenthaceae, approx. 120 species) are carnivorous pitcher plants with a centre of diversity comprising the Philippines, Borneo, Sumatra and Sulawesi. Nepenthes pitchers use three main mechanisms for capturing prey: epicuticular waxes inside the pitcher; a wettable peristome (a collar-shaped structure around the opening); and viscoelastic fluid. Previous studies have provided evidence suggesting that the first mechanism may be more suited to seasonal climates, whereas the latter two might be more suited to perhumid environments. In this study, this idea was tested using climate envelope modelling. METHODS: A total of 94 species, comprising 1978 populations, were grouped by prey capture mechanism (large peristome, small peristome, waxy, waxless, viscoelastic, non-viscoelastic, 'wet' syndrome and 'dry' syndrome). Nineteen bioclimatic variables were used to model habitat suitability at approx. 1 km resolution for each group, using Maxent, a presence-only species distribution modelling program. KEY RESULTS: Prey capture groups putatively associated with perhumid conditions (large peristome, waxless, viscoelastic and 'wet' syndrome) had more restricted areas of probable habitat suitability than those associated putatively with less humid conditions (small peristome, waxy, non-viscoelastic and'dry' syndrome). Overall, the viscoelastic group showed the most restricted area of modelled suitable habitat. CONCLUSIONS: The current study is the first to demonstrate that the prey capture mechanism in a carnivorous plant is constrained by climate. Nepenthes species employing peristome-based and viscoelastic fluid-based capture are largely restricted to perhumid regions; in contrast, the wax-based mechanism allows successful capture in both perhumid and more seasonal areas. Possible reasons for the maintenance of peristome-based and viscoelastic fluid-based capture mechanisms in Nepenthes are discussed in relation to the costs and benefits associated with a given prey capture strategy.

Endeavour, altitude and risk: reflections on a lifetime of mountaineering and exploration.

In July 2012 thousands of competitors from many nations arrive for the London Olympics, each striving to be a champion. Oh, the drive, resolve, heartache and pain. Our capital will be taken over, the press will both celebrate and criticize events; sponsorship deals will soon dominate the results. The men and women who are competing will have trained for many months or years, striven nationally and internationally, fighting hard for places in their teams. What drives them? This short paper is a personal perspective, unashamedly anecdotal, looking at some of the driving forces behind my own endeavours. I have spent a lifetime climbing mountains, with a focus on the exploration of remote regions. I also deal here with the physiological and medical challenges that high altitude mountaineering poses, and discuss its risks.

Tuning of color contrast signals to visual sensitivity maxima of tree shrews by three Bornean highland Nepenthes species.

Three species of Nepenthes pitcher plants (Nepenthes rajah, Nepenthes lowii and Nepenthes macrophylla) specialize in harvesting nutrients from tree shrew excreta in their pitchers. In all three species, nectaries on the underside of the pitcher lid are the focus of the tree shrews' attention. Tree shrews are dichromats, with visual sensitivity in the blue and green wavebands. All three Nepenthes species were shown to produce visual signals, in which the underside of the pitcher lid (the area of highest nectar production) stood out in high contrast to the adjacent area on the pitcher (i.e., was brighter), in the blue and green wavebands visible to the tree shrews. N. rajah showed the tightest degree of "tuning," notably in the green waveband. Conversely, pitchers of Nepenthes burbidgeae, a typical insectivorous species sympatric with N. rajah, did not produce a color pattern tuned to tree shrew sensitivity maxima.

The use of light in prey capture by the tropical pitcher plant Nepenthes aristolochioides.

Nepenthes pitcher plants deploy tube-shaped pitchers to catch invertebrate prey; those of Nepenthes aristolochioides possess an unusual translucent dome. The hypothesis was tested that N. aristolochioides pitchers operate as light traps, by quantifying prey capture under three shade treatments. Flies are red-blind, with visual sensitivity maxima in the UV, blue, and green wavebands. Red celluloid filters were used to reduce the transmission of these wavebands into the interior of the pitchers. Those that were shaded at the rear showed a 3-fold reduction in Drosophila caught, relative to either unshaded control pitchers, or pitchers that were shaded at the front. Thus, light transmitted through the translucent dome is a fundamental component of N. aristolochioides' trapping mechanism.

A unique resource mutualism between the giant Bornean pitcher plant, Nepenthes rajah, and members of a small mammal community.

The carnivorous pitcher plant genus Nepenthes grows in nutrient-deficient substrates and produce jug-shaped leaf organs (pitchers) that trap arthropods as a source of N and P. A number of Bornean Nepenthes demonstrate novel nutrient acquisition strategies. Notably, three giant montane species are engaged in a mutualistic association with the mountain treeshrew, Tupaia montana, in which the treeshrew defecates into the pitchers while visiting them to feed on nectar secretions on the pitchers' lids.Although the basis of this resource mutualism has been elucidated, many aspects are yet to be investigated. We sought to provide insights into the value of the mutualism to each participant. During initial observations we discovered that the summit rat, R. baluensis, also feeds on sugary exudates of N. rajah pitchers and defecates into them, and that this behavior appears to be habitual. The scope of the study was therefore expanded to assess to what degree N. rajah interacts with the small mammal community.We found that both T. montana and R. baluensis are engaged in a mutualistic interaction with N. rajah. T .montana visit pitchers more frequently than R. baluensis, but daily scat deposition rates within pitchers do not differ, suggesting that the mutualistic relationships are of a similar strength. This study is the first to demonstrate that a mutualism exists between a carnivorous plant species and multiple members of a small mammal community. Further, the newly discovered mutualism between R. baluensis and N. rajah represents only the second ever example of a multidirectional resource-based mutualism between a mammal and a carnivorous plant.

Rhythmic delta activity represents a form of nonconvulsive status epilepticus in anti-NMDA receptor antibody encephalitis.

Anti-NMDA receptor antibody encephalitis is a limbic encephalitis with psychiatric manifestations, abnormal movements, coma, and seizures. The coma and abnormal movements are not typically attributed to seizure activity, and slow activity is the most common EEG finding. We report drug-resistant nonconvulsive status epilepticus as the basis for coma in a 19-year-old woman with anti-NMDA receptor antibodies and a mediastinal teratoma. The EEG showed generalized rhythmic delta activity, with evolution in morphology, frequency, and field typical of nonconvulsive status epilepticus. The status was refractory to antiepileptic drugs, repeated drug-induced coma, resection of the tumor, intravenous steroids, rituximab, and plasmapheresis. She awoke after the addition of felbamate, and the rhythmic delta activity ceased. The rhythmic delta activity described with coma in anti-NMDA receptor antibody encephalitis may represent a pattern of status epilepticus in some patients. Felbamate, which has NMDA receptor antagonist activity, should be studied as a therapeutic agent in this condition.

Tetracycline resistance-encoding plasmid from Bacillus sp. strain #24, isolated from the marine sponge Haliclona simulans.

Knowledge of the nature of resistance determinants in natural habitats is fundamental to increasing our understanding of the development of antibiotic resistance in clinical settings. Here we provide the first report of a tetracycline resistance-encoding plasmid, pBHS24, from a marine sponge-associated bacterium, Bacillus sp. strain #24, isolated from Haliclona simulans.

The carnivorous syndrome in Nepenthes pitcher plants: current state of knowledge and potential future directions.

Nepenthes is the largest genus of pitcher plants, with its centre of diversity in SE Asia. The plants grow in substrates that are deficient in N and offset this deficiency by trapping animal prey, primarily arthropods. Recent research has provided new insights into the function of the pitchers, particularly with regard to prey tapping and retention. Species examined to date use combinations of wettable peristomes, wax layers and viscoelastic fluid to trap and retain prey. In many respects, this has redefined our understanding of the functioning of Nepenthes pitchers. In addition, recent research has shown that several Nepenthes species target specific groups of prey animals, or are even evolving away from a strictly carnivorous mode of operation. Future research into nutrient sequestration strategies and mechanisms of prey attraction would no doubt further enhance our knowledge of the ecology of this remarkable genus.

Mutualism between tree shrews and pitcher plants: perspectives and avenues for future research.

Three species of Nepenthes pitcher plants from Borneo engage in a mutualistic interaction with mountain tree shrews, the basis of which is the exchange of nutritional resources. The plants produce modified "toilet pitchers" that produce copious amounts of exudates, the latter serving as a food source for tree shrews. The exudates are only accessible to the tree shrews when they position their hindquarters over the pitcher orifice. Tree shrews mark valuable resources with faeces and regularly defecate into the pitchers when they visit them to feed. Faeces represent a valuable source of nitrogen for these Nepenthes species, but there are many facets of the mutualism that are yet to be investigated. These include, but are not limited to, seasonal variation in exudate production rates by the plants, behavioral ecology of visiting tree shrews, and the mechanism by which the plants signal to tree shrews that their pitchers represent a food source. Further research into this extraordinary animal-plant interaction is required to gain a better understanding of the benefits to the participating species.

Trap geometry in three giant montane pitcher plant species from Borneo is a function of tree shrew body size.

*Three Bornean pitcher plant species, Nepenthes lowii, N. rajah and N. macrophylla, produce modified pitchers that 'capture' tree shrew faeces for nutritional benefit. Tree shrews (Tupaia montana) feed on exudates produced by glands on the inner surfaces of the pitcher lids and defecate into the pitchers. *Here, we tested the hypothesis that pitcher geometry in these species is related to tree shrew body size by comparing the pitcher characteristics with those of five other 'typical' (arthropod-trapping) Nepenthes species. *We found that only pitchers with large orifices and lids that are concave, elongated and oriented approximately at right angles to the orifice capture faeces. The distance from the tree shrews' food source (that is, the lid nectar glands) to the front of the pitcher orifice precisely matches the head plus body length of T. montana in the faeces-trapping species, and is a function of orifice size and the angle of lid reflexion. *Substantial changes to nutrient acquisition strategies in carnivorous plants may occur through simple modifications to trap geometry. This extraordinary plant-animal interaction adds to a growing body of evidence that Nepenthes represents a candidate model for adaptive radiation with regard to nitrogen sequestration strategies.

Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant.

Nepenthes pitcher plants are typically carnivorous, producing pitchers with varying combinations of epicuticular wax crystals, viscoelastic fluids and slippery peristomes to trap arthropod prey, especially ants. However, ant densities are low in tropical montane habitats, thereby limiting the potential benefits of the carnivorous syndrome. Nepenthes lowii, a montane species from Borneo, produces two types of pitchers that differ greatly in form and function. Pitchers produced by immature plants conform to the 'typical' Nepenthes pattern, catching arthropod prey. However, pitchers produced by mature N. lowii plants lack the features associated with carnivory and are instead visited by tree shrews, which defaecate into them after feeding on exudates that accumulate on the pitcher lid. We tested the hypothesis that tree shrew faeces represent a significant nitrogen (N) source for N. lowii, finding that it accounts for between 57 and 100 per cent of foliar N in mature N. lowii plants. Thus, N. lowii employs a diversified N sequestration strategy, gaining access to a N source that is not available to sympatric congeners. The interaction between N. lowii and tree shrews appears to be a mutualism based on the exchange of food sources that are scarce in their montane habitat.

A case of poststreptococcal opsoclonus-myoclonus syndrome.

High antistreptococcal antibody titer (ASOT) was measured in a 31-year-old Caucasian lady presenting with opsoclonus and myoclonus. She was treated with oral steroids and 8 weeks after the onset of symptoms she had a normal ASOT and only mild residual symptoms. This is one of the first cases of opsoclonus-myoclonus syndrome developing, following a streptococcal infection in adults.