Determining patterns of nucleotide and amino acid substitution is the first step during sequence evolution analysis. However, it is not easy to visualize the different phylogenetic signatures ...imprinted in aligned nucleotide and amino acid sequences.
Here we present PoSE (Pattern of Sequence Evolution), a reliable resource for unveiling the evolutionary history of sequence alignments and for graphically displaying their contents. Substitutions are displayed by category (transitions and transversions), codon position, and phenotypic effect (synonymous and nonsynonymous). Visualization is accomplished using MATLAB scripts wrapped around PAML (Phylogenetic Analysis by Maximum Likelihood), implemented in an easy-to-use graphical user interface. The application displays inferred substitutions estimated by baseml or codeml, two programs included in the PAML software package. PoSE organizes patterns of substitution in eleven plots, including estimated non-synonymous/synonymous ratios (dN/dS) along the sequence alignment. In addition, PoSE provides visualization and annotation of patterns of amino acid substitutions along groups of related sequences that can be graphically inspected in a phylogenetic tree window.
PoSE is a useful tool to help determine major patterns during sequence evolution of protein-coding sequences, hypervariable regions, or changes in dN/dS ratios. PoSE is publicly available at https://github.com/CDCgov/PoSE.
Little information is available on host-parasite relationships between bivalves and larval nematodes. Herein, we describe nematode larvae (likely stage 2) in the infraorder Ascaridomorpha infecting ...the foot, intestine, and mantle of a freshwater mussel (Alabama rainbow, Villosa nebulosa Conrad, 1834) and detail histopathological changes to infected tissues. A total of 43 live mussels from the South Fork of Terrapin Creek, Alabama, were collected between 2010 and 2014, with 14 sectioned for histopathology and 29 dissected. Of the 14 sectioned mussels, 5 appeared to be uninfected, and 7, 1, and 1 had histozoic infections observed in the foot and intestine, intestine only, and mantle edge and foot, respectively. Twenty-three of 29 (79%) of the mussels dissected were infected by live nematodes, and mean nematode abundance was 8.3 (CL = 5.23–13), with 2 mussels infected with >100 nematodes each. Thus, with a total of 32 of the 43 collected mussels observed with nematodes, overall infection prevalence was 74.4% (CL = 0.594–0.855). The 18S rDNA of this nematode was 99% similar to that of several ascaridids (species of Kathlaniidae Lane, 1914 and Quimperiidae Baylis, 1930) that mature in aquatic/semi-aquatic vertebrates; the recovered 18S phylogenetic tree indicated this nematode from V. nebulosa shares a recent common ancestor with Ichthyobronema hamulatum (Ascaridomorpha: Quimperiidae; GenBank Accession Number KY476351). Pathological changes to tissue associated with these infections comprised focal tissue damage, but a cellular response was not evident. The Alabama rainbow possibly represents an intermediate or paratenic host. Given these results, the nematode is likely not pathogenic under normal stream conditions; however, high intensity infections in the foot could inhibit pedal extension and retraction; which would have demonstrable health consequences to a freshwater mussel. Based on our review of the bivalve mollusc parasite literature, a collective biodiversity of 61 nematodes reportedly exhibit some degree of symbiosis (from commensal to parasitic) with 21 bivalves (28 nematode spp. from 17 marine bivalve spp.; 33 nematode spp. from 4 freshwater bivalve spp.); only four records exist of putatively parasitic nematodes from Unionida. The present study represents the first description of a nematode species that invades the tissues of a Unionidae species.
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•Pathological changes comprised focal tissue damage but a cellular response to the parasites was not evident.•Nematodes from infected tissues appear to be second stage larvae of Ascaridomorpha.•The small subunit rDNA sequence of this nematode was 99% similar to species of Kathlaniidae and Quimperiidae.•The nematode is likely not pathogenic under normal stream conditions.
Variable platyfish,
Xiphophorus variatus
(Meek, 1904) (Cyprinodontiformes: Poeciliidae) and eastern mosquitofish,
Gambusia holbrooki
Girard, 1859 (Poeciliidae) from earthen ponds in west central ...Florida were examined for parasitic infections. At necropsy, we observed myriad nematodes (adults and eggs), which we identified as
Huffmanela
cf.
huffmani
, infecting the swim bladder, gonad, and visceral peritoneum. Nucleotide sequences (small subunit ribosomal DNA,
18S
) of
H.
cf.
huffmani
from variable platyfish and eastern mosquitofish were identical; likewise for newly obtained
18S
sequences of
Huffmanela huffmani
Moravec, 1987 from the swim bladder of red breast sunfish,
Lepomis auritus
(Linnaeus, 1758) (Centrarchiformes: Centrarchidae) and warmouth,
Lepomis gulosus
(Cuvier, 1829) from the San Marcos River (type locality for
Huffmanela huffmani
Moravec, 1987), Texas. The sequences of
H. huffmani
and
H.
cf.
huffmani
differed by 7 (1%) nucleotides. Pathological changes comprised proliferation of the tunica externa of the swim bladder in low-intensity infections in addition to inflammation, proliferation, and tissue necrosis of swim bladder, peritoneum, and gonad in high-intensity infections. The lesion was severe, affecting the cellular constituents of the swim bladder wall and reducing the size of the swim bladder lumen; potentially reducing swim bladder physiological efficiency. The present study is the first record of a freshwater species of
Huffmanela
Moravec, 1987 from beyond the San Marcos River, first record of a species of
Huffmanela
from a livebearer, first nucleotide sequences and phylogenetic analysis for
Huffmanela
, and first evidence that an infection by a species of
Huffmanela
causes pathological changes that could impact organ function.
Habitat fragmentation has limited the range of the sicklefin redhorse to a few tributaries within these river basins; however, collection records indicate the sicklefin redhorse used to inhabit the ...majority of rivers in the Blue Ridge portion of these river basins (United States Fish and Wildlife Service 2020) The United States Fish and Wildlife Service (USFWS) has ongoing projects to monitor populations of this species throughout its range and to propagate it for reintroduction into its historical habitat, which are currently focused on reintroducing sicklefin redhorse above impoundments in the Oconaluftee and Tuckasegee rivers (Little Tennessee River Basin) (Moyer et al. 2009, United States Fish and Wildlife Service 2020). MATERIALS AND METHODS On 26 June 2018, myxospores consistent with a species of Myxobolus were excised from the skin of two sicklefin redhorses within a closed recirculating aquaculture system at the Warm Springs National Fish Hatchery, Warm Springs, Georgia. After discovering the infection in the captive fish, we initiated field efforts to obtain additional conspecific myxospores for morphology and nucleotide analysis by non-lethal sampling, i.e., biopsy of infected scales and adjacent skin. DNA was extracted from one microscopically/morphologically confirmed isolate of myxospores from each locality (Oconaluftee River and Tuckasegee River), each isolate consisted of myxospores from a single plasmodium, using the DNeasy Blood & Tissue kit (Qiagen) according to the manufacturer's protocol.
Abstract Background Gastrointestinal involvement of non-Hodgkin’s lymphoma (NHL), although rare, may require surgical intervention. The purpose of the current study was to determine the incidence, ...presentation, and management of patients with NHL of the colon or rectum. Methods Demographic data, signs, symptoms, disease stage, and treatment of patients with a primary gastrointestinal lymphoma treated between 1973 and 2005 were identified. Results Forty-three of 244 gastrointestinal lymphoma patients (18%) had colon or rectal involvement. Most common symptoms on presentation were pain (49%), hematochezia (49%), change in bowel habits (23%), and weight loss (19%). Most common site of involvement was the ileocecum. Twenty-six patients (60%) required surgery. The majority (56%) had urgent or emergent operations. Conclusions Colorectal involvement by NHL occurred in 18% of patients with gastrointestinal lymphoma. Surgery was required for pain, obstruction, and/or bleeding. Physicians caring for patients must be aware of the potential need for surgery in treating this patient population.
Myxobolus cerebralis (Bivalvulida: Myxobolidae), the aetiological agent of salmonid whirling disease, was detected in 2 river basins of North Carolina during 2015, which initiated the largest ...spatial–temporal monitoring project for the disease ever conducted within the south‐eastern United States (focused mainly in eastern Tennessee and western North Carolina). A total of 2072 rainbow trout Oncorhynchus mykiss, 1,004 brown trout Salmo trutta and 468 brook trout Salvelinus fontinalis were screened from 113 localities within 7 river basins during June 2017 through October 2019. Infections were detected by pepsin–trypsin digest, microscopy and the species‐specific nested polymerase chain reaction (PCR) in 19 localities across 6 river basins. Myxospore morphology was indistinguishable from the published literature. In 2019, five rainbow trout that symptomatic for whirling disease (sloping neurocranium and lordosis) were captured and processed for histopathology. Myxospores were detected in the calvarial cartilage of two deformed trout with associated erosion of the cartilage consistent with reported whirling disease lesions. This is the first report of M. cerebralis in Tennessee and the first histologically confirmed cases of whirling disease in southern Appalachian (south‐eastern United States) rivers and streams and expands the distribution of M. cerebralis throughout western North Carolina and eastern Tennessee.
Thelohanellus magnacysta n. sp. (Bivalvulida: Myxobolidae) infects the skeletal muscle of blacktail shiner, Cyprinella venusta Girard, 1856 (Cypriniformes: Cyprinidae) in Bull Creek, Chattahoochee ...River Basin, eastern Georgia. Although numerous members of ThelohanellusKudo, 1933 have overlapping myxospore dimensions with the new species, it differs from all nominal congeners by polar filament coil number and polar capsule width as well as by lacking a mucous envelope, iodinophilic vacuole, and sutural markings. With the use of novel primers for Myxozoa, a phylogenetic analysis of the small subunit ribosomal DNA (SSU rDNA) suggests that the new species shares a recent common ancestor with a clade of cyprinid-infecting species of Myxobolus Bütschli, 1882 (Bivalvulida: Myxobolidae) and Thelohanellus. Consistent with other published research concerning the systematics of Thelohanellus, this result suggested that Thelohanellus and Myxobolus are polyphyletic and need revision. Histological sections of infected blacktail shiners confirmed that myxospores were only found within a plasmodium and only infected skeletal muscle and that plasmodia were encapsulated by a granuloma comprising varying degrees of acute granulomatous inflammation. The new species is the fourth of Thelohanellus reported from North America and the first reported from Cyprinella, as well as the first myxozoan described from the blacktail shiner.
The following study suggests that the recrational services sector represents a growing, yet currently understudied, opportunity in the area of international services marketing. For example, personal ...consumption expenditures in the United States have increased from $50 billion in 1985 to $246.8 billion in 1988. Parry suggests that European consumers have also been presented with an increasingly eclectic array of recreational alternatives during the last decade.
The rise in automobiles within rapidly developing nations in Sub-Saharan Africa necessitates the exploration of sustainable transportation alternatives, especially in urban regions. Walking and ...cycling are essential active modes of transport that can improve city residents’ well-being and economic vitality. However, their adoption as mobility choices depends on infrastructure limitations and residents’ perception of their safety. This study investigates the impact of socio-demographic and neighborhood characteristics on the safety perception of active mobility within the Accra metropolis of Ghana. The study utilized survey data on residents’ mobility habits and willingness to use active transport modes for daily commutes. Most of the respondents are permanent residents of Accra, and 51% are between 18–35 years old. The developed random parameter ordered logit model reveals that the perception of safety varies across the population and is influenced by respondents’ demographic characteristics and neighborhood configuration. Notably, factors related to walking duration to bus stops, income level, and household size, unplanned neighborhoods, among others, decrease residents’ safety perception of active mobility. The study offers valuable insights that can aid in planning future urban active mobility systems in Accra to establish safer and more sustainable transportation choices for the city’s residents.
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