Citizen science initiatives document biodiversity baselines at an urban lake

Changes to biodiversity from urbanization are occurring worldwide, and baseline data is vital to document the magnitude and direction of these alterations. We set out to document the biodiversity of an urban lake in Eastern Iowa that was devoid of baseline data prior to a renovation project that will convert the site into a major area for human recreation. Throughout the course of one year, we studied the biodiversity at Cedar Lake utilizing the citizen-science application iNaturalist coupled with semi-structured BioBlitz events, which we compared to previous opportunistic observations at the site. From a semi-structured approach to document biodiversity with citizen science, our analyses revealed more diverse community metrics over a shorter period compared to more than a decade of prior observations.

Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.

There's a frog in my salad! A review of online media coverage for wild vertebrates found in prepackaged produce in the United States

Prepackaged leafy green vegetables represent one of the fastest growing segments of the fresh-produce industry in the United States. Several steps in the production process have been mechanized to meet the downstream demand for prebagged lettuces. The growth in this market, however, has come with drawbacks, and chief among them are consumers finding wild animals in prepackaged crops. These incidents may signal an overburdened produce supply chain, but we currently lack the information needed to determine if this is a food-safety problem or food-quality concern. Here, we address this gap by reviewing online media coverage of wild vertebrates found in prepackaged produce items by customers in the United States. We discovered 40 independent incidents since 2003 with 95% having occurred during 2008-2018, suggesting that the frequency of incidents may have increased during the last decade. The minority of incidents included wild animals found in organic produce (27.5%), whereas the majority involved conventionally grown crops (72.5%). Most incidents involved amphibians (52.5%) and reptiles (22.5%), while fewer contained mammals (17.5%) and birds (7.5%). Frogs and toads made up all of the amphibian-related incidents, with more than 60% comprising small-bodied treefrogs found in various types of fresh leafy greens. At least seven incidents involved Pacific Treefrogs (Hyliola regilla) and three comprised Green Anoles (Anolis carolinensis). One lizard and nine frogs were found alive, and at least two frogs were released into non-native areas. This is the first review quantifying incidents of vertebrates found by customers in prepackaged produce, yet it remains unclear whether these occurrences indicate a food-safety crisis or a complaint against food quality. Nevertheless, wild animals can spread diseases to humans via contaminated produce, therefore we contend that industry professionals can reduce the potential health risk to their consumers and negative economic consequences to themselves through increased attention to this matter.

Evolutionary history of burrowing asps (Lamprophiidae: Atractaspidinae) with emphasis on fang evolution and prey selection

Atractaspidines are poorly studied, fossorial snakes that are found throughout Africa and western Asia, including the Middle East. We employed concatenated gene-tree analyses and divergence dating approaches to investigate evolutionary relationships and biogeographic patterns of atractaspidines with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). We sampled 91 individuals from both atractaspidine genera (Atractaspis and Homoroselaps). Additionally, we used ancestral-state reconstructions to investigate fang and diet evolution within Atractaspidinae and its sister lineage (Aparallactinae). Our results indicated that current classification of atractaspidines underestimates diversity within the group. Diversification occurred predominantly between the Miocene and Pliocene. Ancestral-state reconstructions suggest that snake dentition in these taxa might be highly plastic within relatively short periods of time to facilitate adaptations to dynamic foraging and life-history strategies.

Cryptic diversity in Rhampholeon boulengeri (Sauria: Chamaeleonidae), a pygmy chameleon from the Albertine Rift biodiversity hotspot

Several biogeographic barriers in the Central African highlands have reduced gene flow among populations of many terrestrial species in predictable ways. Yet, a comprehensive understanding of mechanisms underlying species divergence in the Afrotropics can be obscured by unrecognized levels of cryptic diversity, particularly in widespread species. We implemented a multilocus phylogeographic approach to examine diversity within the widely distributed Central African pygmy chameleon, Rhampholeon boulengeri. Gene-tree analyses coupled with a comparative coalescent-based species delimitation framework revealed R. boulengeri as a complex of at least six genetically distinct species. The spatiotemporal speciation patterns for these cryptic species conform to general biogeographic hypotheses supporting vicariance as the main factor behind patterns of divergence in the Albertine Rift, a biodiversity hotspot in Central Africa. However, we found that parapatric species and sister species inhabited adjacent habitats, but were found in largely non-overlapping elevational ranges in the Albertine Rift, suggesting that differentiation in elevation was also an important mode of divergence. The phylogeographic patterns recovered for the genus-level phylogeny provide additional evidence for speciation by isolation in forest refugia, and dating estimates indicated that the Miocene was a significant period for this diversification. Our results highlight the importance of investigating cryptic diversity in widespread species to improve understanding of diversification patterns in environmentally diverse regions such as the montane Afrotropics.

Wild snakes harbor West Nile virus

West Nile virus (WNV) has a complex eco-epidemiology with birds acting as reservoirs and hosts for the virus. Less well understood is the role of reptiles, especially in wild populations. The goal of our study was to determine whether a wild population of snakes in Pennsylvania harbored WNV. Six species of snakes were orally sampled in the summer of 2013 and were tested for the presence of WNV viral RNA using RT-PCR. Two Eastern Garter Snakes, Thamnophis sirtalis sirtalis tested positive for viral RNA (2/123, 1.62%). These results indicate a possible role for snakes in the complex transmission cycle of WNV.

Rescuing Perishable Neuroanatomical Information from a Threatened Biodiversity Hotspot: Remote Field Methods for Brain Tissue Preservation Validated by Cytoarchitectonic Analysis, Immunohistochemistry, and X-Ray Microcomputed Tomography

Biodiversity hotspots, which harbor more endemic species than elsewhere on Earth, are increasingly threatened. There is a need to accelerate collection efforts in these regions before threatened or endangered species become extinct. The diverse geographical, ecological, genetic, morphological, and behavioral data generated from the on-site collection of an individual specimen are useful for many scientific purposes. However, traditional methods for specimen preparation in the field do not permit researchers to retrieve neuroanatomical data, disregarding potentially useful data for increasing our understanding of brain diversity. These data have helped clarify brain evolution, deciphered relationships between structure and function, and revealed constraints and selective pressures that provide context about the evolution of complex behavior. Here, we report our field-testing of two commonly used laboratory-based techniques for brain preservation while on a collecting expedition in the Congo Basin and Albertine Rift, two poorly known regions associated with the Eastern Afromontane biodiversity hotspot. First, we found that transcardial perfusion fixation and long-term brain storage, conducted in remote field conditions with no access to cold storage laboratory equipment, had no observable impact on cytoarchitectural features of lizard brain tissue when compared to lizard brain tissue processed under laboratory conditions. Second, field-perfused brain tissue subjected to prolonged post-fixation remained readily compatible with subsequent immunohistochemical detection of neural antigens, with immunostaining that was comparable to that of laboratory-perfused brain tissue. Third, immersion-fixation of lizard brains, prepared under identical environmental conditions, was readily compatible with subsequent iodine-enhanced X-ray microcomputed tomography, which facilitated the non-destructive imaging of the intact brain within its skull. In summary, we have validated multiple approaches to preserving intact lizard brains in remote field conditions with limited access to supplies and a high degree of environmental exposure. This protocol should serve as a malleable framework for researchers attempting to rescue perishable and irreplaceable morphological and molecular data from regions of disappearing biodiversity. Our approach can be harnessed to extend the numbers of species being actively studied by the neuroscience community, by reducing some of the difficulty associated with acquiring brains of animal species that are not readily available in captivity.

Charles Bonnet syndrome: a literature review into diagnostic criteria, treatment and implications for nursing practice

Charles Bonnet syndrome is a disease of vision which may be mistakenly identified as manifestations of psychosis and consequently be treated by psychiatrists and mental health nurses rather than ophthalmologists. This literature review considers current understanding of the syndrome, its treatment and the role of mental health nurses. The two main findings of the review are that despite a long recognition of the syndrome, diagnostic criteria are not established and that there is no recognized evidence-based medical treatment. As well as this, two novel treatments which may offer future benefits are discussed. Current best practice is identified as identifying the condition and providing reassurance and education, a role that mental health nurses that are aware of Charles Bonnet syndrome can fulfil perhaps better than any other discipline.

Histology of the terminal ileum in coeliac disease

BACKGROUND

The histological lesion of gluten sensitivity primarily affects the proximal small bowel. The purpose of this study was to assess whether there were features of gluten-sensitive enteropathy in biopsies taken from the terminal ileum during colonoscopy/ileoscopy. Specific and sensitive abnormalities might facilitate diagnosis of coeliac disease in patients undergoing colonoscopy as their initial procedure or help select those who should proceed to upper gastrointestinal endoscopy and duodenal biopsy.

METHODS

Terminal ileal biopsies, taken from 30 patients with duodenal villous atrophy consistent with coeliac disease and from 60 control patients with no evidence of coeliac or inflammatory bowel disease, were reviewed blindly and compared. Biopsies were assessed for the presence or absence of villous atrophy and crypt hyperplasia, and counts were made of intraepithelial lymphocytes (IELs).

RESULTS

One patient only, in the coeliac group, had partial villous atrophy with crypt hyperplasia in the terminal ileum. IEL counts were significantly higher (P< 0.005) in the coeliac group than among controls (mean per 100 enterocytes 26 versus 10). An ileal IEL count > or =25 had a sensitivity for duodenal villous atrophy (VA) of 60% and specificity of 100%.

CONCLUSIONS

Coeliac disease may affect the entire small bowel. Increased IEL density in the terminal ileum is associated with duodenal VA and should prompt a search for coeliac disease by serology and duodenal biopsy. Conversely, a normal IEL count does not allow the exclusion of coeliac disease with confidence.

Transthyretin values correlate with mucosal recovery in patients with coeliac disease taking a gluten free diet

AIMS

To assess changes in indicators of nutrition and iron deficiency as possible non-invasive markers of mucosal recovery in patients with coeliac disease on a gluten free diet.

METHODS

Concentrations of transthyretin, retinol binding protein, soluble transferrin receptor, IgA anti-gliadin, and IgA anti-transglutaminase, and titres of IgA anti-endomysial antibody were measured in 36 newly diagnosed adult patients with coeliac disease and duodenal villous atrophy before (T0) and after one year (T1) on a gluten free diet. Duodenal biopsies taken at T0 and T1 were compared and graded as no improvement (no change in initial grade of villous atrophy) or improvement.

RESULTS

Twenty two patients showed histological improvement and 14 showed no improvement. Transthyretin values increased in all patients with mucosal improvement and decreased in all patients showing no improvement. However, transthyretin values did not correlate with the degree of villous atrophy at T0 and T1 when assessed separately. Changes in retinol binding protein and soluble transferrin receptor values did not correlate with mucosal improvement. Coeliac disease associated antibodies (to gliadin, endomysium, and transglutaminase) decreased in most patients between T0 and T1, irrespective of mucosal recovery.

CONCLUSIONS

Serial but not single measurements of transthyretin may be used as a non-invasive test to monitor mucosal recovery and therefore reduce the need for, or frequency of, follow up biopsies in treated patients with coeliac disease.

Sensitivity of serum tissue transglutaminase antibodies for endomysial antibody positive and negative coeliac disease

BACKGROUND

Serum antibodies to tissue transglutaminase (tTGA) are reported to have high sensitivity and specificity for coeliac disease and to correlate closely with endomysial antibodies (EmA). We assessed their performance in a coeliac population with a high proportion of EmA-negative patients, who have been under-represented in previous studies.

METHODS

We used a commercial ELISA kit to test for IgA class tTGA in sera from a population of 73 untreated coeliac patients with normal serum IgA and a high percentage (19%) EmA-negative, taking 58 patients with normal duodenal biopsies as controls. EmA was measured using indirect immunofluorescence.

RESULTS

Forty-six (63%) patients with villous atrophy (VA) had both tTGA and EmA. However, when considered separately, sensitivities of tTGA and EmA for VA were similar (75% versus 81%) and both had high specificity (98% versus 97%). As 9 patients were tTGA-positive only and 13 had EmA only, selection of patients for biopsy on the presence of either antibody would have had a sensitivity of 93% (68 of 73), with 5 (7%) patients seronegative for both.

CONCLUSION

Although the ELISA tTGA assay is more convenient than EmA testing, it offers no advantages in sensitivity or specificity if used in isolation. However, incomplete concordance between EmA and tTGA positivity means that combination screening with both assays offers higher sensitivity, as almost a third of patients have only one antibody. As some coeliac patients with normal serum IgA are negative for both antibodies, biopsies should still be performed in seronegative individuals deemed at high risk for coeliac disease.

Disappearance of endomysial antibodies in treated celiac disease does not indicate histological recovery

OBJECTIVE

Although serum IgA-class endomysial antibody (EmA) has high sensitivity for villous atrophy (VA) in patients with untreated celiac disease, few studies have attempted to correlate EmA seroconversion with histological recovery after starting a gluten-free diet. We prospectively studied changes in EmA status and in duodenal histology of seropositive patients after dietary treatment.

METHODS

Patients with VA and EmA had repeat EmA testing at 3, 6, and 12 months after starting gluten-free diet, plus assessment of dietary compliance by dietitians and follow-up duodenal biopsy at 12 months. VA before and after treatment was classified as partial (P), subtotal (ST), and total (T).

RESULTS

Of 77 patients with newly diagnosed VA and without IgA deficiency, 62 (81%) had EmA: 46 of 57 (81%) with T or STVA and 16 of 20 (80%) with PVA. Of 53 initially EmA-positive patients who completed study criteria, EmA was undetectable in 31 patients (58%) after 3 months' diet, in 40 (75%) after 6 months, and in 46 (87%) after 12 months. However, only 21 patients (40%), all seronegative by 12 months, had complete villous recovery. Only three (33%) of 10 patients with persisting ST or TVA and two (9%) of 22 with PVA remained EmA positive. Four of the five patients with persisting EmA had poor dietary compliance.

CONCLUSIONS

EmA is a poor predictor of persisting VA after patients have started gluten-free diet, although it may be of value in monitoring dietary compliance. Although there are no clear guidelines regarding the need for follow-up biopsy, EmA seroconversion cannot substitute. The apparent association between dietary compliance and seroconversion suggests that gluten intake may determine whether untreated celiac patients are EmA positive or negative for a given degree of small bowel damage.

Reliance on serum endomysial antibody testing underestimates the true prevalence of coeliac disease by one fifth

BACKGROUND

Although IgA endomysial antibody (EmA) is currently the serologic test of choice in selecting suspected coeliac patients for duodenal biopsies, false-negative cases have been reported and may be more common than previous studies suggest. We assessed the sensitivity of EmA for patients with biopsy-confirmed villous atrophy (VA).

METHODS

We studied 89 patients without IgA deficiency for whom biopsy had not been primarily prompted by a positive EmA result. VA was graded as partial, subtotal, or total (PVA, STVA, TVA). Serum EmA was assayed with indirect immunofluorescence.

RESULTS

The sensitivity of EmA for VA was 78% (69 of 89) and was similar for PVA (79%) and ST/TVA (77%). Only 4 of the 20 EmA-negative patients had increased serum IgA-class antigliadin antibody levels as measured with enzyme-linked immunosorbent assay. All seronegative patients who complied with dietary gluten exclusion responded clinically, with histologic improvement after 12 months in 8 (67%) of 12 patients who had follow-up biopsies.

CONCLUSIONS

EmA-negative coeliac disease is common. Reliance on EmA testing to select patients for biopsy will result in significant underdiagnosis.

Identification of coeliac disease in primary care

BACKGROUND

Coeliac disease is common yet often undiagnosed because symptoms may be trivial, non-specific, or non-gastrointestinal, or because of lack of clinician awareness. Serum IgA-class endomysial antibodies (EmA) have high specificity for coeliac disease and may facilitate case-finding by clinicians other than gastroenterologists. We assessed the appropriateness and diagnostic yield of of requests for EmA by primary care general practitioners in a defined geographic area of Northern Ireland.

METHODS

We identified patients who had EmA examination requests by their general practitioners during 1994-1996. Individual patient questionnaires were posted to the general practitioners concerned, seeking information on indications for testing, management after the result, and final diagnosis. We compared new patient diagnosis rates in two catchment areas, one served by a large district general hospital with, and the other by smaller hospitals without, a medical gastroenterology facility.

RESULTS

A total of 239 patients had coeliac profile testing by 69 of 177 general practitioners in the area. Data were available for 181 patients not previously known to have coeliac disease, of whom 20 (11%) had EmA. All EmA-positive patients were referred to hospital, where 19 underwent small-bowel biopsy, which confirmed coeliac disease in all 19. Only 7 (35%) of the 20 had diarrhoea, and there was no significant difference in EmA prevalence among patients tested with and without diarrhoea. Although the mean number of new patients (per 100,000 population annually) diagnosed by biopsy was 11 at the large hospital compared with 5 elsewhere, the numbers identified by EmA in general practice for the 2 catchment areas were similar (2 and 3, respectively).

CONCLUSION

General practitioners have an important role in the identification of patients with coeliac disease, particularly where there is no local medical gastroenterology facility, and this is facilitated by EmA testing.

Possible role of Helicobacter pylori serology in reducing endoscopy workload

We validated a commercial enzyme-linked immunosorbent assay (ELISA), Helico-G, in diagnosing H. pylori in 129 patients (mean age 50 years, range 15-86). We analysed the results of endoscopy against serology to see whether there was a possibility of adopting the strategy of not endoscoping dyspeptic subjects under the age of 45. H. pylori infection was considered present if either histology and/or culture were positive. The ELISA had a sensitivity of 88%, specificity of 72%, positive predictive value of 85%, negative predictive value of 77% and accuracy of 82% in detecting H. pylori. In a subgroup of 52 subjects aged 45 or less (mean age 35 years, range 15-45), 17 out of 25 patients with positive endoscopic findings were H. pylori seropositive while 16 out of 27 patients had normal endoscopic findings. Eighteen out of the 52 patients (35%) were H. pylori seronegative and normal endoscopically except for five patients (10%) who had mild to moderate oesophagitis and two who had non-erosive gastritis (4%). All patients with duodenal ulcer disease (7) were seropositive giving predictive values of positive and negative serology for a diagnosis of duodenal ulcer disease as 28% and 100%, respectively. Therefore adopting a strategy of endoscoping subjects under the age of 45 only if they were H. pylori seropositive would have saved 35% of endoscopies in this age group but missed oesophagitis in 10%. Negative serology would tend to exclude duodenal ulcer disease while positive serology discriminates poorly for it. Serology may be a useful adjunct in screening to reduce endoscopy workload provided that patients with gastro-oesophageal reflux symptoms are excluded.

Fatal lung abscess due to Lactobacillus casei ss rhamnosus

A fatal case of community acquired pneumonia due to Lactobacillus casei ss rhamnosus is reported. Clinicians should be aware of this type of pneumonia.

Pseudosarcomatous lesions of the urinary bladder

The clinical, microscopical, immunocytochemical and ultrastructural features of five cases of benign mesenchymal proliferative lesions of the urinary bladder, mimicking sarcoma, are presented. Four of the five patients are alive and disease-free following diagnosis, an interval ranging from 9 months to 9 years, mean 4 years. A fifth patient, who had a pseudosarcomatous stromal response adjacent to a urinary transitional cell carcinoma, now has invasive transitional cell carcinoma. The lesions revealed a striking microscopical, immunocytochemical and ultrastructural similarity to nodular fasciitis, suggesting the lesions represented a bizarre mesenchymal proliferative response to inflammation.

Carcinoma in Crohn's disease of the colon

Two cases of carcinoma in Crohn's disease of the colon are reported. One patient was a 30-year-old man who had asymptomatic Crohn's ileocolitis resulting in an acute presentation due to toxic dilatation of the colon. This was preceded by a short prodromal period of four weeks, characterized by intermittent diarrhea on the basis of a coloileal tumor fistula. A mucus-secreting adenocarcinoma was present in the sigmoid colon associated with both adjacent and one nearby focus of high-grade mucosal dysplasia. Pelvic wall and abdominal metastases were present, and the patient died two months later. The other patient was a 60-year-old woman who had a nine-year history of biopsy-proven Crohn's proctocolitis. A stricture of the sigmoid colon due to Crohn's disease also harbored an invasive adenocarcinoma. The carcinoma was not evident preoperatively or on initial gross pathologic examination. The presentation and pathology of large intestinal carcinoma in Crohn's colitis are discussed and illustrated.

Metronidazole in prevention and treatment of bacteroides infections in elective colonic surgery

A double-blind randomised trial was carried out among 46 patients undergoing elective colonic surgery; 27 patients received prophylactic metronidazole and 19 received placebo. Anaerobic infections did not develop in any of the metronidazole-treated patients, but did develop in 11 (58%) of 19 controls who were subsequently successfully treated with metronidazole.

Power spectral distribution of the masseter electromyogram from surface electrodes

The power spectral distribution of an electromyogram offers a useful presentation of the myoelectric signal at any level of muscle activity. Various factors which may affect this distribution are considered. A computerized method for obtaining the power spectral distribution for masseter and a study of the effect of bite force and electrode position on this is described.