Nantucket Cottage Hospital

BACKGROUND: Babesiosis is a tick-borne, malaria-like illness known to be enzootic in southern New England. A course of clindamycin and quinine is the standard treatment, but this regimen frequently causes adverse reactions and occasionally fails. A promising alternative treatment is atovaquone plus azithromycin. METHODS: We conducted a prospective, nonblinded, randomized trial of the two regimens in 58 subjects with non-life-threatening babesiosis on Nantucket, on Block Island, and in southern Connecticut. The subjects were assigned to receive either atovaquone (750 mg every 12 hours) and azithromycin (500 mg on day 1 and 250 mg per day thereafter) for seven days (40 subjects) or clindamycin (600 mg every 8 hours) and quinine (650 mg every 8 hours) for seven days (18 subjects). RESULTS: Adverse effects were reported by 15 percent of the subjects who received atovaquone and azithromycin, as compared with 72 percent of those who received clindamycin and quinine (P<0.001). The most common adverse effects with atovaquone and azithromycin were diarrhea and rash (each in 8 percent of the subjects); with clindamycin and quinine the most common adverse effects were tinnitus (39 percent), diarrhea (33 percent), and decreased hearing (28 percent). Symptoms had resolved three months after the start of therapy in 65 percent of those who received atovaquone and azithromycin and 73 percent of those who received clindamycin and quinine (P=0.66), and after six months no patient in either group had symptoms. Three months after the completion of the assigned regimen, no parasites could be seen on microscopy, and no Babesia microti DNA was detected in the blood of any subject. CONCLUSIONS: For the treatment of babesiosis, a regimen of atovaquone and azithromycin is as effective as a regimen of clindamycin and quinine and is associated with fewer adverse reactions.

To determine whether a unique group of clinical and laboratory manifestations characterize certain major deer tick-transmitted human pathogens in North America, we compared the symptoms, short-term complications, and laboratory test results of New England residents who became ill due to > or =1 of these pathogens. Patients completed a uniformly structured questionnaire and submitted blood samples for serologic and polymerase chain reaction (PCR) testing after developing symptoms of Lyme disease, human babesiosis, or human granulocytic ehrlichiosis (HGE). Complete blood count with thin blood smear, PCR, and immunoglobulin M antibody tests helped differentiate the acute manifestations of these diseases. Physicians should consider use of tests designed to diagnose babesiosis and HGE in patients with Lyme disease who experience a prolonged flulike illness that fails to respond to appropriate antiborrelial therapy.

Human infection due to Babesia microti has been regarded as infrequent and a condition primarily affecting the elderly or immunocompromised. To determine whether risk in endemic sites may be increasing relative to that of Borrelia burgdorferi and to define its age-related clinical spectrum, we carried out a 10-year community-based serosurvey and case finding study on Block Island, Rhode Island. Less intensive observations were conducted in nearby sites. Incidence of babesial infection on Block Island increased during the early 1990s, reaching a level about three-fourths that of borrelial infection. The sera of approximately one-tenth of Block Island residents reacted against babesial antigen, a seroprevalence similar to those on Prudence Island and in southeastern Connecticut. Although the number and duration of babesial symptoms in people older than 50 years of age approximated those in people 20 to 49 years of age, more older adults were admitted to hospital than younger adults. Few Babesia-infected children were hospitalized. Babesial incidence at endemic sites in southern New England appears to have risen during the 1990s to a level approaching that due to borreliosis.

BACKGROUND: The first recognized cases of Borrelia miyamotoi disease (BMD) in North America were reported in the northeastern United States in 2013. OBJECTIVE: To further describe the clinical spectrum and laboratory findings for BMD. DESIGN: Case series. SETTING: Patients presenting to primary care offices, emergency departments, or urgent care clinics in 2013 and 2014. PARTICIPANTS: Acutely febrile patients from the northeastern United States in whom the treating health care providers suspected and ordered testing for tick-transmitted infections. MEASUREMENTS: Whole-blood polymerase chain reaction (PCR) testing was performed for the presence of specific DNA sequences of common tickborne infections (including BMD). Serologic testing for B. miyamotoi was performed using a recombinant glycerophosphodiester phosphodiesterase (rGlpQ) protein. Clinical records were analyzed to identify the major features of acute disease. RESULTS: Among 11,515 patients tested, 97 BMD cases were identified by PCR. Most of the 51 case patients on whom clinical histories were reviewed presented with high fever, chills, marked headache, and myalgia or arthralgia. Twenty-four percent were hospitalized. Elevated liver enzyme levels, neutropenia, and thrombocytopenia were common. At presentation, 16% of patients with BMD were seropositive for IgG and/or IgM antibody to B. miyamotoi rGlpQ. Most (78%) had seropositive convalescent specimens. Symptoms resolved after treatment with doxycycline, and no chronic sequelae or symptoms were observed. LIMITATION: Findings were based on specimens submitted for testing to a reference laboratory, and medical records of only 51 of the 97 case patients with BMD were reviewed. CONCLUSION: Patients with BMD presented with nonspecific symptoms, including fever, headache, chills, myalgia, and arthralgia. Laboratory confirmation of BMD was possible by PCR on blood from acutely symptomatic patients who were seronegative at presentation. Borrelia miyamotoi disease may be an emerging tickborne infection in the northeastern United States. PRIMARY FUNDING SOURCE: IMUGEN.

BACKGROUND: Chronic plantar fasciitis is a common orthopedic condition that can prove difficult to successfully treat. In this study, autologous platelet-rich plasma (PRP), a concentrated bioactive blood component rich in cytokines and growth factors, was compared to traditional cortisone injection in the treatment of chronic cases of plantar fasciitis resistant to traditional nonoperative management. METHODS: Forty patients (23 females and 17 males) with unilateral chronic plantar fasciitis that did not respond to a minimum of 4 months of standardized traditional nonoperative treatment modalities were prospectively randomized and treated with either a single ultrasound guided injection of 3 cc PRP or 40 mg DepoMedrol cortisone. American Orthopedic Foot and Ankle Society (AOFAS) hindfoot scoring was completed for all patients immediately prior to PRP or cortisone injection (pretreatment = time 0) and at 3, 6, 12, and 24 months following injection treatment. Baseline pretreatment radiographs and MRI studies were obtained in all cases to confirm the diagnosis of plantar fasciitis. RESULTS: The cortisone group had a pretreatment average AOFAS score of 52, which initially improved to 81 at 3 months posttreatment but decreased to 74 at 6 months, then dropped to near baseline levels of 58 at 12 months, and continued to decline to a final score of 56 at 24 months. In contrast, the PRP group started with an average pretreatment AOFAS score of 37, which increased to 95 at 3 months, remained elevated at 94 at 6 and 12 months, and had a final score of 92 at 24 months. CONCLUSIONS: PRP was more effective and durable than cortisone injection for the treatment of chronic recalcitrant cases of plantar fasciitis. LEVEL OF EVIDENCE: Level I, prospective randomized comparative series.

BACKGROUND: Chronic Achilles tendinosis is a relatively common but difficult orthopedic condition to treat. In this study, autologous platelet rich plasma (PRP), a concentrated bioactive blood component rich in cytokines and growth factors, was evaluated to determine its potential long-term efficacy in treating chronic cases of Achilles tendinosis resistant to traditional nonoperative management. METHODS: Thirty patients with chronic Achilles tendinosis who did not respond to a minimum of 6 months of traditional nonoperative treatment modalities were treated with a single ultrasound guided injection of PRP. AOFAS scoring was completed for all patients pretreatment and at 0, 1, 2, 3, 6, 12, and 24 months post-treatment. MRI and/or ultrasound studies were completed for all patients pre-treatment and at 6 months post-treatment. Prior to the PRP treatment all of the patients in this study were considering surgical Achilles repair for their severe symptoms. RESULTS: The average AOFAS score increased from 34 (range, 20 to 60) to 92 (range, 87 to 100) by 3 months after PRP treatment and remained elevated at 88 (range, 76 to 100) at 24 months post-treatment. Pretreatment imaging abnormalities present in the Achilles tendon on MRI and ultrasound studies resolved in 27 of 29 patients at 6 months post-treatment. Clinical success was achieved in 28 of 30 patients. CONCLUSION: Platelet-rich plasma was used effectively to treat chronic recalcitrant cases of Achilles tendinosis.

Between 20 July and 15 Octoboer 1975, five cases of human infection with Babesia microti were diagnosed on Nantucket Island, Massachusetts. The illness was characterized by fever, drenching sweats, shaking chills, myalgia, arthralgia, extreme fatigue, and a mild-to-moderate hemolytic anemia. None of the patients had a history of splenetomy. Although all patients responded symptomatically to treatment with oral chloroquine phosphate, parasitemia and fatigue frequently persisted for several weeks to months.

Salinity data from the Atlantic continental shelf off New England indicate that the freshwater/saltwater interface is far out of equilibrium with modern sea-level conditions. More than 150 km offshore of Long Island, New York, aquifer salinity levels are less than 5 parts per thousand (5 ppt). Salinity levels within confining units beneath Nantucket Island, Massachusetts, are 30%–70% of seawater levels and exhibit a parabolic profile consistent with ongoing vertical diffusion. Here, we evaluate two fluid-flow-inducing mechanisms that could explain the apparent flushing of these coastal-plain aquifers: (1) meteoric recharge during Pleistocene sea-level lowstands, and (2) subglacial recharge from the Laurentide Ice Sheet.&#13;\n&#13;\nAnalytical models of vertical solute diffusion for the Nantucket confining units suggest that flushing of aquifers beneath Nantucket began in the late Pleistocene between ca. 195 and 21 ka; the models assume a diffusion coefficient of 3.0 × 10−11 m2/s. Cross-sectional numerical models of variable-density groundwater flow, heat, and solute transport could not reproduce the relatively low-salinity groundwaters observed off Long Island by applying boundary conditions consistent with Pleistocene sea-level fluctuations. Observed salinity conditions were most closely matched in the models by also including the effects of subglacial recharge from the Laurentide Ice Sheet and allowing groundwater to discharge from Miocene aquifers along submarine canyons near the continental slope. Simulated recharge induced by Laurentide Ice Sheet meltwater was probably short lived but, on average, about two to ten times greater than modern subaerial levels. A sensitivity analysis performed using our cross-sectional model suggests that a narrow range of hydrologic conditions can drive fresh water long distances offshore across the continental shelf.

Significance Invasive species are often expected to benefit from novel conditions encountered with global change. Our range models based on demography show that invasive Alliaria petiolata (garlic mustard) may have much lower establishment in New England under future climate, despite prolific success under current climate, whereas other invasive and native plants may expand their ranges. Forecasts suggest that management should focus on inhibiting northward spread of A. petiolata into unoccupied areas and understanding source–sink population dynamics and how community dynamics might respond to loss of A. petiolata (it modifies soil properties). Our methods illustrate inadequacy of current approaches to forecasting invasions in progress, which are based on correlations between species’ occurrence and environment and illustrate critical need for mechanistic studies.

Borrelia miyamotoi sensu lato, a relapsing fever Borrelia sp., is transmitted by the same ticks that transmit B. burgdorferi (the Lyme disease pathogen) and occurs in all Lyme disease-endemic areas of the United States. To determine the seroprevalence of IgG against B. miyamotoi sensu lato in the northeastern United States and assess whether serum from B. miyamotoi sensu lato-infected persons is reactive to B. burgdorferi antigens, we tested archived serum samples from area residents during 1991-2012. Of 639 samples from healthy persons, 25 were positive for B. miyamotoi sensu lato and 60 for B. burgdorferi. Samples from ≈10% of B. miyamotoi sensu lato-seropositive persons without a recent history of Lyme disease were seropositive for B. burgdorferi. Our results suggest that human B. miyamotoi sensu lato infection may be common in southern New England and that B. burgdorferi antibody testing is not an effective surrogate for detecting B. miyamotoi sensu lato infection.

Background: The conventional 2-tiered serologic testing protocol for Lyme disease (LD), an enzyme immunoassay (EIA) followed by immunoglobulin M and immunoglobulin G Western blots, performs well in late-stage LD but is insensitive in patients with erythema migrans (EM), the most common manifestation of the illness. Western blots are also complex, difficult to interpret, and relatively expensive. In an effort to improve test performance and simplify testing in early LD, we evaluated several modified 2-tiered testing (MTTT) protocols, which use 2 assays designed as first-tier tests sequentially, without the need of Western blots. Methods: The MTTT protocols included (1) a whole-cell sonicate (WCS) EIA followed by a C6 EIA; (2) a WCS EIA followed by a VlsE chemiluminescence immunoassay (CLIA); and (3) a variable major protein-like sequence, expressed (VlsE) CLIA followed by a C6 EIA. Sensitivity was determined using serum from 55 patients with erythema migrans; specificity was determined using serum from 50 patients with other illnesses and 1227 healthy subjects. Results: Sensitivity of the various MTTT protocols in patients with acute erythema migrans ranged from 36% (95% confidence interval [CI], 25%-50%) to 54% (95% CI, 42%-67%), compared with 25% (95% CI, 16%-38%) using the conventional protocol (P = .003-0.3). Among control subjects, the 3 MTTT protocols were similarly specific (99.3%-99.5%) compared with conventional 2-tiered testing (99.5% specificity; P = .6-1.0). Conclusions: Although there were minor differences in sensitivity and specificity among MTTT protocols, each provides comparable or greater sensitivity in acute EM, and similar specificity compared with conventional 2-tiered testing, obviating the need for Western blots.

ABSTRACT Despite being identified as an essential scientific practice, argumentation is rarely integrated into instruction. This could be influenced by teachers’ pedagogical design capacity (PDC), which considers teaching as a design activity influenced by both instructional resources (such as tools and professional development (PD)) and teacher resources (such as beliefs and pedagogical content knowledge (PCK)). In this study, we investigated how the development of five upper elementary and middle school teachers’ beliefs and PCK impacted their design and integration of argumentation within their instruction. Data sources included pre‐ and postsurveys, videotaped lessons, and interviews. Our analyses resulted in two groups of teachers. While several teachers offloaded some of their lesson design by using PD resources, others adapted the PD resources and renamed an aspect of their current instruction as argumentation. Moreover, the teachers who offloaded some of their lesson design exhibited argumentation within their instruction and greater change in their beliefs or PCK for argumentation. This suggests the importance of future teacher education experiences supporting teachers’ PDC by providing multiple opportunities to offload, try out, and reflect on instruction. Future research should explore whether teachers understanding of the PDC framework supports their understanding of argumentation.

Brief Communications15 August 1995Human Granulocytic Ehrlichiosis in MassachusettsSam R. Telford, Timothy J. Lepore, Patricia Snow, Cynthia K. Warner, and Jacqueline E. DawsonSam R. TelfordFrom Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia., Timothy J. LeporeFrom Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia., Patricia SnowFrom Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia., Cynthia K. WarnerFrom Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia., and Jacqueline E. DawsonFrom Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia.Author, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-123-4-199508150-00006 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Two new tick-borne zoonoses have recently emerged as threats to public health in North America. Both are caused by infection with Ehrlichia species, obligate intracellular bacteria that localize within the phagosomes of leukocytes. The spectrum of illness varies from mild to severe; about one third of patients require hospitalization. Persons exposed to ticks may present with a "spotless spotted fever" or a disease similar to Lyme disease that does not feature erythema and is accompanied by fever, chills, severe headache, myalgia, malaise, and nausea. A maculopapular or petechial rash, however, may be present [1, 2]. Laboratory findings include thrombocytopenia, leukopenia, ...References1. Fishbein DB, Kemp A, Dawson JE, Greene NR, Redus MA, Fields DH. Human ehrlichiosis: prospective active surveillance in febrile hospitalized patients. J Infect Dis. 1989; 160:803-9. Google Scholar2. Fishbein DB, Dawson JE, Robinson LE. Human ehrlichiosis in the United States, 1985 to 1990. Ann Intern Med. 1994; 120:736-43. Google Scholar3. Donatien A, Lestoquard F. Existence in Algerie d'une rickettsia du chien. Bull Soc Pathol Exot. 1935; 28:418-9. Google Scholar4. Misao T, Kobayashi Y. Studies on infectious mononucleosis (glandular fever). I. Isolation of the etiologic agent from blood, bone marrow, and lymph node of a patient with infectious mononucleosis by using mice. Kyushu J Med Sci. 1955; 6:145-52. Google Scholar5. Maeda K, Markowitz N, Hawley RC, Ristic M, Cox D, McDade JE. Human infection with Ehrlichia canis, a leukocytic rickettsia. N Engl J Med. 1987; 316:853-6. Google Scholar6. Dawson JE, Anderson BE, Fishbein DB, Sanchez JL, Goldsmith CS, Wilson KH, et al. Isolation and characterization of an Ehrlichia sp. from a patient diagnosed with human ehrlichiosis. J Clin Microbiol. 1991; 29:2741-5. Google Scholar7. Anderson BE, Dawson JE, Jones DC, Wilson KH. Ehrlichia chaffeensis, a new species associated with human ehrlichiosis. J Clin Microbiol. 1991; 29:2838-42. Google Scholar8. Bakken JS, Dumler JS, Chen SM, Eckman MR, Van Etta LL, Walker DH. Human granulocytic ehrlichiosis in the upper Midwest United States. A new species emerging? JAMA. 1994; 272:212-8. Google Scholar9. Chen SM, Dumler JS, Bakken JS, Walker DH. Identification of a granulocytotropic Ehrlichia species as the etiologic agent of human disease. J Clin Microbiol. 1994; 32:589-95. Google Scholar10. Lillie RD. Histopathologic Technique. Philadelphia: Blakiston; 1948:300. Google Scholar11. Krause PJ, Telford SR 3d, Ryan R, Conrad PA, Wilson M, Thomford JW, et al. Diagnosis of babesiosis: evaluation of a serologic test for the detection of Babesia microti antibody. J Infect Dis. 1994; 169:923-6. Google Scholar12. Rosa Brunet L, Sellitto C, Spielman A, Telford SR III. Natural immune competence of the white footed mouse reservoir of the agent of Lyme disease. Infect. Immunity. 1995; (In press). Google Scholar13. Dawson JE, Stallknecht DE, Howerth EW, Warner C, Biggie K, Davidson WR, et al. Susceptibility of white-tailed deer (Odocoileus virginianus) to infection with Ehrlichia chaffeensis, the etiologic agent of human ehrlichiosis. J Clin Microbiol. 1994; 32:2724-8. Google Scholar14. Rynkiewicz DL, Liu LX. Human ehrlichiosis in New England (Letter). N Engl J Med. 1994; 330:292-3. Google Scholar15. Brouqui P, Raoult D. Human ehrlichiosis (Letter). N Engl J Med. 1994; 330:1760-1. Google Scholar16. Telford SR III, Dawson JE, Spielman A. Prevalence of antibody to Ehrlichia chaffeensis in residents of a Massachusetts Lyme disease focus (Abstract). Program and Abstracts of the 41st Annual Meeting of the American Society of Tropical Medicine and Hygiene. Am J Trop Med Hyg. 1992; 47:249. Google Scholar17. Rich SM, Caporale DA, Telford SR III, Kocher TD, Hartl DL, Spielman A. Distribution of the Ixodes ricinus-like ticks of eastern North America. Proc Natl Acad Sci U S A. 1995; (In press). Google Scholar18. Pancholi P, Kolbert CP, Mitchell P, Reed K, Dumler SJ, Bakken JS, et al. Ixodes dammini as a potential vector of human granulocytic ehrlichiosis. J Infect Dis. (In press). Google Scholar Author, Article, and Disclosure InformationAuthors: Sam R. Telford; Timothy J. Lepore; Patricia Snow; Cynthia K. Warner; Jacqueline E. DawsonAffiliations: From Harvard School of Public Health, Boston, Massachusetts. Nantucket Cottage Hospital, Nantucket, Massachusetts. The Centers for Disease Control and Prevention, Atlanta, Georgia.Corresponding Author: Sam R. Telford III, DSc, Department of Tropical Public Health, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115.Acknowledgments: The authors thank R.E. Corstvet for supplying antigen slides, and Vanesa Baker for technical assistance.Grant Support: By National Institutes of Health grant AI19693, Smith Kline Beecham Pharmaceuticals, the Chace Fund, and the Gibson Island Corporation. 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Human babesiosis is an emerging tick-borne disease caused by the intraerythrocytic protozoan Babesia microti. Its geographic distribution is more limited than that of Lyme disease, despite sharing the same tick vector and reservoir hosts. The geographic range of babesiosis is expanding, but knowledge of its range is incomplete and relies exclusively on reports of human cases. We evaluated the utility of tick-based surveillance for monitoring disease expansion by comparing the ratios of the 2 infections in humans and ticks in areas with varying B. microti endemicity. We found a close association between human disease and tick infection ratios in long-established babesiosis-endemic areas but a lower than expected incidence of human babesiosis on the basis of tick infection rates in new disease-endemic areas. This finding suggests that babesiosis at emerging sites is underreported. Vector-based surveillance can provide an early warning system for the emergence of human babesiosis.

BACKGROUND: Babesia microti, the most frequently implicated pathogen in transfusion-transmitted babesiosis, is widely endemic in the Northeast and upper Midwestern United States. High seroprevalence in endemic areas limits antibody-based donor screening. A high-performance molecular test is needed to identify donors in the preseroconversion window phase as well as to discriminate past serologic exposure with parasite clearance from continued parasitemia. STUDY DESIGN AND METHODS: Frozen Babesia-spiked whole blood was microcentrifuged, and the supernatant transferred and microcentrifuged again to concentrate the parasite. The DNA was extracted and amplified using real-time polymerase chain reaction (PCR) using Babesia-specific primers. The assay was employed in three series of experiments: 1) a validation and optimization spiking experiment, 2) a blinded serial dilution probit analysis to determine the limit of detection, and 3) evaluation of two blinded panels of clinical samples from possible babesiosis cases. RESULTS: At a decreasing inoculum of 445, 44.5, and 4.45 copies/mL, the assay had positive rates of 100, 97.5, and 81%, respectively. The blinded probit analysis demonstrated a detection rate of 95 and 50% at 12.92 and 1.52 parasites/2 mL of whole blood, respectively. Evaluation of clinical samples showed 13 of 21 samples to be positive, with a range of 85 to 4.8 million parasites/mL. There were no positives detected among 48 healthy donors CONCLUSION: We have developed a highly sensitive and specific, quantitative real-time PCR-based assay for detection of B. microti that could have a useful role in blood screening. It can also be employed broadly to understand Babesia epidemiology, disease pathogenesis, and host immunology.

A 48-year-old woman was bitten by a tick on Nantucket Island, Massachusetts, and developed a fever. Babesia microti were recognized in her erythrocytes. Transmission to rodents confirmed the diagnosis of babesiosis. This is the sixth reported example of this malaria-like, tick-transmitted disease and the second to occur on Nantucket. The patient had not received transfusions or traveled to an endemic malaria area. Hemolytic anemia, present in this case, was the cause of death in three previously reported cases. Chloroquine therapy was successful in eradicating the parasites in this patient, the third survivor.

BACKGROUND: Viruses and small-genome bacteria (~2 megabases and smaller) comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG) is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms. FINDINGS: CGUG is available at http://binf.gmu.edu/geneorder.html as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes. CONCLUSION: CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.

Babesia microti, the primary cause of human babesiosis in the United States, is transmitted by Ixodes scapularis ticks; transmission may also occur through blood transfusion and transplacentally. Most infected people experience a viral-like illness that resolves without complication, but those who are immunocompromised may develop a serious and prolonged illness that is sometimes fatal. The geographic expansion and increasing incidence of human babesiosis in the northeastern and midwestern United States highlight the need for high-throughput sensitive and specific assays to detect parasites in both ticks and humans with the goals of improving epidemiological surveillance, diagnosis of acute infections, and screening of the blood supply. Accordingly, we developed a B. microti-specific quantitative PCR (qPCR) assay (named BabMq18) designed to detect B. microti DNA in tick and human blood samples using a primer and probe combination that targets the 18S rRNA gene of B. microti. This qPCR assay was compared with two nonquantitative B. microti PCR assays by testing tick samples and was found to exhibit higher sensitivity for detection of B. microti DNA. The BabMq18 assay has a detection threshold of 10 copies per reaction and does not amplify DNA in I. scapularis ticks infected with Babesia odocoilei, Borrelia burgdorferi, Borrelia miyamotoi, or Anaplasma phagocytophilum. This highly sensitive and specific qPCR assay can be used for detection of B. microti DNA in both tick and human samples. Finally, we report the prevalence of B. microti infection in field-collected I. scapularis nymphs from three locations in southern New England that present disparate incidences of human babesiosis.

Carbon and nitrogen isotope ratios of (1) bone collagen from six burials of the Late Woodland Period at Nantucket Island, Massachusetts, and (2) a wide range of potential dietary materials provide data for evaluating coastal diets. Archaeological and historical data give evidence for the availability and use of dietary items. The bases of the food chains and trophic levels define the possible food groups: terrestrial C 3 and C 4 plants and their consumers, marine C 3 and C 4 -like plants and their consumers, and marine carnivores. From these data, computer analysis of multiple linear mixing equations relating isotope ratios of human bone collagen to those of dietary food groups shows allowable ranges of these food groups in the diet. The results argue for a diet of 40–65 percent oceanic animals, with the rest consisting of substantial amounts of animals from salt marsh and eelgrass meadows or of maize, and minor amounts of C3 plants and their consumers.

Limited information is available on streams in the Adirondack region of New York, although streams are more prone to acidification than the more studied Adirondack lakes. A stream assessment was therefore undertaken in the Oswegatchie and Black River drainages; an area of 4585 km(2) in the western part of the Adirondack region. Acidification was evaluated with the newly developed base-cation surplus (BCS) and the conventional acid-neutralizing capacity by Gran titration (ANC(G)). During the survey when stream water was most acidic (March 2004), 105 of 188 streams (56%) were acidified based on the criterion of BCS < 0 microeq L(-1), whereas 29% were acidified based on an ANC(G) value < 0 microeq L(-1). During the survey when stream water was least acidic (August 2003), 15 of 129 streams (12%) were acidified based on the criterion of BCS < 0 microeq L(-1), whereas 5% were acidified based on ANC(G) value < 0 microeq L(-1). The contribution of acidic deposition to stream acidification was greater than that of strongly acidic organic acids in each of the surveys by factors ranging from approximately 2 to 5, but was greatest during spring snowmelt and least during elevated base flow in August. During snowmelt, the percentage attributable to acidic deposition was 81%, whereas during the October 2003 survey, when dissolved organic carbon (DOC) concentrations were highest, this percentage was 66%. The total length of stream reaches estimated to be prone to acidification was 718 km out of a total of 1237 km of stream reaches that were assessed.