Tracking animal movements via collaborative acoustic telemetry networks: Multiscale habitat use, phenology, and management insights.

Estuaries support diverse fish and invertebrate communities, including resident species that rely on estuarine habitats year-round and transient migratory species. The unique movement patterns of these animals connect habitats within and far beyond the estuary and are integrally linked to fisheries management objectives. With a focus on Chesapeake Bay, this study leveraged data from collaborative acoustic telemetry networks in the northwest Atlantic to assess habitat use and phenology of movements for seven species of fish (cownose rays, dusky sharks, smooth dogfish, alewife, striped bass, common carp, and blue catfish) and one invertebrate (horseshoe crabs).

Early detection and recovery of river herring spawning habitat use in response to a mainstem dam removal.

Historical loss of river and stream habitats due to impassable dams has contributed to the severe decline of many fish species. Anadromous fishes that migrate from the sea to freshwater streams to spawn have been especially impacted as dams restrict these fish from accessing ancestral spawning grounds. In 2018, Bloede Dam was removed from the Patapsco River near Baltimore, Maryland, restoring approximately 100 km of potential habitat for migratory fish.

Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species.

Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as 'river herring'), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations).

Women's health training in gastroenterology fellowship: a national survey of fellows and program directors.

Background And Aims: The Gastroenterology Core Curriculum requires training in women's digestive disorders; however, requirements do not necessarily produce knowledge and competence. Our study goals were: (1) to compare perceptions of education, fellow-reported levels of competence, and attitudes towards training in women's gastrointestinal (GI) health issues during fellowship between gastroenterology fellows and program directors, and (2) to determine the barriers for meeting training requirements.

Methods: A national survey assessing four domains of training was conducted.

Utility of colonoscopy in the evaluation of diarrhea in solid organ transplant recipients.

Background: Diarrhea is common in solid organ transplant recipients. Colonoscopy with random biopsies is performed frequently in the diagnostic evaluation of the posttransplant population with diarrhea. The purpose of this study was to determine the sensitivity of colonoscopy with random biopsy in determining a specific diagnosis and changing management in solid organ transplant recipients with diarrhea.

Biologic study of the effects of octreotide-LAR on growth hormone in unresectable and metastatic hepatocellular carcinoma.

Background: Animal models suggest that growth hormone participates in hepatocarcinogenesis.

Objective: To correlate the effect of octreotide long-acting release (LAR) on insulin-like growth factor-I (IGF-I) and -II (IGF-II) with response and survival in patients with unresectable and metastatic hepatocellular carcinoma.

Methods: We conducted a phase II, single-institution trial of octreotide-LAR (30 mg intramuscularly every 4 weeks) in 15 patients while monitoring serum IGF-I and -II levels.

Consensus characterization of 16 FMR1 reference materials: a consortium study.

Fragile X syndrome, which is caused by expansion of a (CGG)(n) repeat in the FMR1 gene, occurs in approximately 1:3500 males and causes mental retardation/behavioral problems. Smaller (CGG)(n) repeat expansions in FMR1, premutations, are associated with premature ovarian failure and fragile X-associated tremor/ataxia syndrome. An FMR1-sizing assay is technically challenging because of high GC content of the (CGG)(n) repeat, the size limitations of conventional PCR, and a lack of reference materials available for test development/validation and routine quality control.

Development of genomic reference materials for Huntington disease genetic testing.

Purpose: Diagnostic and predictive testing for Huntington disease requires an accurate measurement of CAG repeats in the HD (IT15) gene. However, precise repeat sizing can be technically challenging, and is complicated by the lack of quality control and reference materials (RM). The aim of this study was to characterize genomic DNA from 14 Huntington cell lines available from the National Institute of General Medical Sciences Human Genetic Cell Repository at the Coriell Cell Repositories for use as reference materials for CAG repeat sizing.

Advances in Huntington's disease diagnostics: development of a standard reference material.

Huntington's disease (HD) is a neurodegenerative disease that affects four to seven individuals per 100,000. The onset of symptoms usually begins in middle age, although approximately 5% become symptomatic as juveniles. Death occurs approximately 15 years following the onset of symptoms, which include choreic movements, cognitive decline and psychiatric changes.

Genetically characterized positive control cell lines derived from residual clinical blood samples.

Background: Positive control materials for clinical diagnostic molecular genetic testing are in critically short supply. High-quality DNA that closely resembles DNA isolated from patient specimens can be obtained from Epstein-Barr virus (EBV)-transformed peripheral blood lymphocyte cell lines. Here we report the development of a process to (a) recover residual blood samples with clinically important mutations detected during routine medical care, (b) select samples likely to provide viable lymphocytes for EBV transformation, (c) establish stable cell lines and confirm the reported mutation(s), and (d) validate the cell lines for use as positive controls in clinical molecular genetic testing applications.

Comparison of the complete mtDNA genome sequences of human cell lines--HL-60 and GM10742A--from individuals with pro-myelocytic leukemia and leber hereditary optic neuropathy, respectively, and the inclusion of HL-60 in the NIST human mitochondrial DNA standard reference material--SRM 2392-I.

Forensic and clinical laboratories benefit from DNA standard reference materials (SRMs) that provide the quality control and assurance that their results from sequencing unknown samples are correct. Therefore, the mitochondrial DNA (mtDNA) genome of HL-60, a promyelocytic leukemia cell line, has been completely sequenced by four laboratories and will be available to the forensic and medical communities in the spring of 2003; it will be called National Institute of Standards and Technology (NIST) SRM 2392-I. NIST human mtDNA SRM 2392 will continue to be available and includes the DNA from two apparently healthy individuals.

Standardization of PCR amplification for fragile X trinucleotide repeat measurements.

To provide the clinical diagnostics community with accurate protocols and measurements for the detection of genetic disorders, we have established a quantitative measurement program for trinucleotide repeats associated with human disease. In this study, we have focused on the triplet repeat associated with fragile X syndrome. Five cell lines obtained from the Coriell Cell Repository were analyzed after polymerase chain reaction (PCR) amplification and size separation.

Objective psychomotor skills assessment of experienced, junior, and novice laparoscopists with virtual reality.

Objective assessment of psychomotor skills in surgery is now a priority; however, this assessment is difficult to achieve because of measurement difficulties associated with the reliability and validity of assessing surgical skills in vivo and in the laboratory. In this study virtual reality (VR) was used to overcome these problems in the objective psychomotor assessment of senior, junior, and novice laparoscopists. Twelve experienced laparoscopic surgeons (performed >50 Minimal Access Surgery (MAS) procedures), 12 inexperienced laparoscopic surgeons (<10 MAS procedures), and 12 laparoscopic novices (no MAS procedures) participated in the study.

A review of the DNA standard reference materials developed by the National Institute of Standards and Technology.

The Standard Reference Materials Program at the US National Institute of Standards and Technology (NIST) has three human DNA standard reference materials (SRM 2390, SRM 2391a, and SRM 2392) currently available [1, 2]. Both the DNA profiling SRM 2390 and the polymerase chain reaction (PCR)-based DNA profiling SRM 2391a are intended for use in forensic and paternity identifications, for instructional law enforcement, or for non-clinical research purposes and are not intended for clinical diagnostics. The mitochondrial DNA (mtDNA) SRM 2392 is to provide standardization and quality control when performing PCR and sequencing any segment or the entire 16,569 base pairs that comprise human mitochondrial DNA.

RFLP band size standards: NIST standard reference material 2390.

The procedural standard for DNA profiling developed by the U.S. advisory board on DNA quality assurance methods mandates annual confirmation of forensic DNA measurement systems against an appropriate reference material supplied by or traceable to the National Institute of Standards and Technology (NIST).

Long PCR for VNTR analysis.

The Polymerase Chain Reaction (PCR) has revolutionized the analysis of DNA from a variety of sources. With its sensitivity and ability to amplify degraded DNAs and small quantities of samples, coupled with fast turn-around-time, PCR is often the analytical method of choice for DNA profiling in forensic laboratories. RFLP methods, while requiring larger amounts of high molecular weight DNA and needing approximately 6-8 weeks of analytical time, still provide a higher power of discrimination per locus than that achieved using the loci currently available for PCR.

Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole.

Rubredoxins (Rds) may be separated into two classes based upon the correlation of their reduction potentials with the identity of residue 44; those with Ala44 have reduction potentials that are approximately 50 mV higher than those with Val44. The smaller side chain volume occupied by Ala44 relative to that occupied by Val44 has been proposed to explain the increase in the reduction potential, based upon changes in the Gly43-Ala44 peptide bond orientation and the distance to the [Fe(SCys)(4)] center in the Pyrococcus furiosus (Pf) Rd crystal structure compared to those of Gly43-Val44 in the Clostridium pasteurianum (Cp) Rd crystal structure. As an experimental test of this hypothesis, single-site Val44 <--> Ala44 exchange mutants, [V44A]Cp and [A44V]Pf Rds, have been cloned and expressed.

Cognitive decline in ageing: are AAMI and AACD distinct entities?

Background: Two sets of research diagnostic criteria, age-associated memory impairment (AAMI) and ageing-associated cognitive decline (AACD), are widely used to describe mild cognitive decline in ageing. However, the extent to which the nosological entities they represent are similar or distinct is unclear.

Methods: A sample of 111 participants without dementia but with informant evidence of cognitive decline were drawn from the EUGERIA Study of Cognitive Ageing, a population-based study in southern France.

Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: beta-sheet chimeras.

The contributions to thermostability of interactions within the beta-sheet region of rubredoxins (Rds) were investigated by examining proteins in which beta-strand sequences of Rds from the hyperthermophilic archaeon Pyrococcus furiosus (Pf) and the mesophilic bacterium Clostridium pasteurianum (Cp) were interchanged. The thermostabilities of the chimeric Rds were assessed by monitoring the decay of the visible absorbance at 490 nm and of the far-UV CD vs time at 92 degrees C. The chimeric Rds Pf15 Cp47 Pf (Pf Rd residues 2-15 and 48-54 and Cp Rd residues 16-47) and Cp15 Pf47 Cp were both found to be far less thermostable than wild-type Pf Rd, indicating that neither the beta-sheet residues (2-7, 10-15, and 48-53) nor the "core residues" (16-47) of Pf Rd independently confer Pf Rd-like thermostability.

2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.

Based on 2D 1H-1H and 2D and 3D 1H-15N NMR spectroscopies, complete 1H NMR assignments are reported for zinc-containing Clostridium pasteurianum rubredoxin (Cp ZnRd). Complete 1H NMR assignments are also reported for a mutated Cp ZnRd, in which residues near the N-terminus, namely, Met 1, Lys 2, and Pro 15, have been changed to their counterparts, (-), Ala and Glu, respectively, in rubredoxin from the hyperthermophilic archaeon, Pyrococcus furiosus (Pf Rd). The secondary structure of both wild-type and mutated Cp ZnRds, as determined by NMR methods, is essentially the same.

Quantitation of optic disc cupping.

In population-based studies and in clinical practice a reliable, objective measure of optic disc cupping is needed. This measure is of special importance when following patients with diagnosed or suspected glaucoma. We have developed a new system using stereoscopic fundus photographs for quantitating optic disc cupping from these photographs.