medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata.

MOTIVATION: Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software. RESULTS: We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019). AVAILABILITY AND IMPLEMENTATION: The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Screening of Living Kidney Donors for Genetic Diseases Using a Comprehensive Genetic Testing Strategy.

Related living kidney donors (LKDs) are at higher risk of end-stage renal disease (ESRD) compared with unrelated LKDs. A genetic panel was developed to screen 115 genes associated with renal diseases. We used this panel to screen six negative controls, four transplant candidates with presumed genetic renal disease and six related LKDs. After removing common variants, pathogenicity was predicted using six algorithms to score genetic variants based on conservation and function. All variants were evaluated in the context of patient phenotype and clinical data. We identified causal variants in three of the four transplant candidates. Two patients with a family history of autosomal dominant polycystic kidney disease segregated variants in PKD1. These findings excluded genetic risk in three of four relatives accepted as potential LKDs. A third patient with an atypical history for Alport syndrome had a splice site mutation in COL4A5. This pathogenic variant was excluded in a sibling accepted as an LKD. In another patient with a strong family history of ESRD, a negative genetic screen combined with negative comparative genomic hybridization in the recipient facilitated counseling of the related donor. This genetic renal disease panel will allow rapid, efficient and cost-effective evaluation of related LKDs.

Taurine, an osteocyte metabolite, protects against oxidative stress-induced cell death and decreases inhibitors of the Wnt/ß-catenin signaling pathway.

Taurine has been shown to have positive effects on bone mass, which are thought to be due in part to its cytoprotective effects on osteoblasts and here we show that taurine also protects osteocytes against cell death due to reactive oxygen species. Using the IDG-SW3 cell line, the expression of the taurine uptake transporter Taut/Slc6a6 is increased during osteoblast to osteocyte differentiation. Taurine had no effect on genes associated with osteoblast to osteocyte differentiation such as Dmp1, Phex or osteocalcin, even at high doses, but a slight yet significant inhibition of alkaline phosphatase was observed at the highest dose (50 mM). No effect was seen on the osteoclast regulatory genes Rankl and Opg, however the wnt antagonist Sost/sclerostin was potently and dose-dependently downregulated in response to taurine supplementation. Taurine also significantly inhibited Dkk1 mRNA expression, but only at 50 mM. Interestingly, osteocytes were found to also be able to synthesize taurine intracellularly, potentially as a self-protective mechanism, but do not secrete the metabolite. A highly significant increase in the expression of cysteine dioxygenase (Cdo), a key enzyme necessary for the production of taurine, was observed with osteoblast to osteocyte differentiation along with a decrease in methionine, the precursor of taurine. For the first time, we describe the synthesis of taurine by osteocytes, potentially to preserve viability and to regulate bone formation through inhibition of sclerostin.

Three Drosophila beta-tubulin sequences: a developmentally regulated isoform (beta 3), the testis-specific isoform (beta 2), and an assembly-defective mutation of the testis-specific isoform (B2t8) reveal both an ancient divergence in metazoan isotypes and structural constraints for beta-tubulin function.

The genomic DNA sequence and deduced amino acid sequence are presented for three Drosophila melanogaster beta-tubulins: a developmentally regulated isoform beta 3-tubulin, the wild-type testis-specific isoform beta 2-tubulin, and an ethyl methanesulfonate-induced assembly-defective mutation of the testis isoform, B2t8. The testis-specific beta 2-tubulin is highly homologous to the major vertebrate beta-tubulins, but beta 3-tubulin is considerably diverged. Comparison of the amino acid sequences of the two Drosophila isoforms to those of other beta-tubulins indicates that these two proteins are representative of an ancient sequence divergence event which at least preceded the split between lines leading to vertebrates and invertebrates. The intron/exon structures of the genes for beta 2- and beta 3-tubulin are not the same. The structure of the gene for the variant beta 3-tubulin isoform, but not that of the testis-specific beta 2-tubulin gene, is similar to that of vertebrate beta-tubulins. The mutation B2t8 in the gene for the testis-specific beta 2-tubulin defines a single amino acid residue required for normal assembly function of beta-tubulin. The sequence of the B2t8 gene is identical to that of the wild-type gene except for a single nucleotide change resulting in the substitution of lysine for glutamic acid at residue 288. This position falls at the junction between two major structural domains of the beta-tubulin molecule. Although this hinge region is relatively variable in sequence among different beta-tubulins, the residue corresponding to glu 288 of Drosophila beta 2-tubulin is highly conserved as an acidic amino acid not only in all other beta-tubulins but in alpha-tubulins as well.

The beta 3-tubulin gene of Drosophila melanogaster is essential for viability and fertility.

We have previously shown that the beta 3-tubulin gene of Drosophila melanogaster encodes a divergent isoform expressed in a complex developmental pattern. The beta 3 gene is transiently expressed in the embryo and again in the pupa at high levels in the developing musculature, and at lower levels in several different pupal tissues of ectodermal origin. Adult expression is confined to specific somatic cells in the gonads. In some of the cell types in which it is expressed, beta 3 is the sole or predominant beta-tubulin, while in others the beta 3 protein is a minor component of the beta-tubulin pool. The sites and timing of beta 3 expression demonstrated that beta 3-tubulin is utilized primarily in cytoplasmic microtubule arrays involved in changes in cell shape and tissue organization, and suggested to us that this isoform may be functionally specialized. To determine whether the expression of the beta 3 gene is essential for normal development, and to examine the specific functions of this divergent isoform, we have generated mutations within the gene. We determined that the small deficiency Df(2R)Px2, which deletes the 60C5,6-60D9,10 region of chromosome 2, removes all of the beta 3 coding sequences, and that the distal breakpoint of the deficiency is approximately 2 kb upstream from the start of transcription of the beta 3 gene. We have generated a total of 31 ethyl methanesulfonate- or diepoxybutane-induced recessive lethal or visible mutations which map within the deficiency. These mutations define 12 new lethal complementation groups, which together with two previously identified visible mutations, altogether identify 14 genes in this interval of the second chromosome. A lethal complementation group comprising mutations in the beta 3-tubulin gene (beta Tub60D) was identified by rescue of their lethality by a wild-type copy of the gene introduced into the genome via P element-mediated germ line transformation. Analysis of the homozygous and transheterozygous phenotypes of the five beta 3 mutations recovered (alleles designated B3t1-B3t5) demonstrates that beta 3-tubulin is essential for viability and fertility.

Increased rate of P300 latency prolongation with age in schizophrenia. Electrophysiological evidence for a neurodegenerative process.

BACKGROUND: The latency of the P300 event-related potential is prolonged in disorders associated with neural damage and degeneration and also becomes prolonged in the course of neural changes that accompany aging. We tested whether the rate of P300 latency increase with age was greater in male schizophrenic patients than in normal subjects because a steeper slope in schizophrenia would suggest a progressive neurodegenerative process. We also evaluated a subset of these subjects for changes in brain volumes as determined by magnetic resonance imaging. METHOD: The P300 component was elicited during an auditory "oddball" paradigm and was recorded from 47 male patients with chronic schizophrenia whose mean age at onset was 22.4 years and from 47 age-, handedness-, and gender-matched control subjects. The relation of P300 latency and amplitude to age within each group was evaluated using correlation and regression analyses. Brain volumes determined via magnetic resonance imaging were evaluated by quantitative volumetric analyses of images acquired with three-dimensional Fourier transform and double echo-spin echo-pulse sequences. RESULTS: The slope of P300 latency on age was steeper for schizophrenic patients than for normal control subjects at midline frontal and central electrode sites. The slope of N100 latency did not differ, implying that the P300 differences were not likely to be due to peripheral hearing loss or damage affecting the initial stages of neural processing. Posterior superior temporal gyrus gray matter volume determined via magnetic resonance imaging significantly diminished with age on the left side in patients with schizophrenia but not on the right side or in controls; these slopes were not, however, statistically significantly different from each other. CONCLUSIONS: These findings provide preliminary evidence that male patients with chronic schizophrenia experience a neurodegenerative process that becomes evident in adulthood and is reflected by the rate of change of P300 latency with age. Whether this process is due to the primary effects of schizophrenia or is secondary to factors associated with schizophrenia's chronic course and treatment remains a question for future investigation.

Review of drug interference with urine glucose tests.

Many drugs have been reported to interfere with copper-reduction or glucose oxidase tests used to measure urine glucose. However, only a few drugs or drug classes have been well documented to clinically interfere with these tests. The interfering drugs include ascorbic acid, beta-lactam antibiotics (e.g., cephalosporins and penicillins), levodopa, and salicylates. Several other drugs may also interfere with certain urine glucose tests, but the interactions are poorly documented. These drugs include chloral hydrate, hyaluronidase, nalidixic acid, nitrofurantoin, p-aminosalicylic acid, phenazopyridine, probenecid, and X-ray contrast media. Drugs or their metabolites that are strong reducing substances produce false-positive results by the copper-reduction method and false-negative results by the glucose oxidase method. The beta-lactam antibiotics interfere with copper-reduction tests by producing copper compounds of various colors that confuse interpretation of test results. Tables are provided that summarize the drug interferences discussed.

Stimulus novelty differentially affects attentional allocation in PTSD.

BACKGROUND: This study investigated attentional allocation in 39 Vietnam combat veterans, 25 with and 14 without posttraumatic stress disorder, assessing P300 amplitudes and latencies during both three-tone and novelty "oddball" tasks. METHODS: The three-tone oddball task consisted of three stimuli: frequent tones (85%), rare target tones (7.5%), and rare distractor tones (7.5%). The novelty oddball task was identical to the three-tone task except that the rare distractor tones were replaced with nonrepeating novel sounds (7.5%). RESULTS: Combat veterans with posttraumatic stress disorder showed significant P300 amplitude enhancements at frontal sites in response to distracting stimuli during the novelty but not during the three-tone oddball tasks. There were no amplitude differences in target tones during either task. CONCLUSIONS: The data suggest that combat veterans with posttraumatic stress disorder demonstrate P300 responses consistent with a heightened orientation response to novel, distracting stimuli. This finding is consistent both with the clinical presentation of the disorder and with theoretical notions that individuals with posttraumatic stress disorder demonstrate information-processing biases towards vague or potentially threatening stimuli.

The effect of family status and schizotypy on electrophysiologic measures of attention and semantic processing.

BACKGROUND: Disturbances in both attention and language are central to the phenomenology of the schizophrenia spectrum disorders. The purpose of this study was to investigate the relative contributions of two factors, family status and schizotypy, on electrophysiologic measures of attention and semantic processing in family members of individuals with schizophrenia. METHODS: Fifteen first-degree relatives of individuals with schizophrenia and 15 comparison subject controls participated in diagnostic evaluations, an assessment of schizotypy, and two event-related potential (ERP) paradigms. The first paradigm was an auditory P300 "oddball" task designed to assess attentional functioning. The second was an N400 sentence paradigm particularly sensitive to language processing. RESULTS: Both relatives and individuals higher in schizotypy, but not their respective comparison groups, showed reductions in P300 amplitude. In the N400 paradigm, individuals higher in schizotypy, but not relatives, showed a reduced N400 effect. There were no differences in latency for either group on either component. CONCLUSIONS: The results suggest that both family status and schizotypal presentation independently contribute to disturbances in electrophysiologic measures sensitive to attention and language. Whereas higher levels of schizotypy appear to be associated with disturbances in both attention and language processing, family membership appears to place individuals at risk for attentional deficits alone.

Neuropsychological correlates of MRI temporal lobe abnormalities in schizophrenia.

OBJECTIVE: The authors evaluated the neuropsychological correlates of temporal lobe abnormalities in schizophrenic patients. METHOD: Fifteen schizophrenic patients underwent assessment of memory, by the Wechsler Memory Scale--Revised, and abstraction/categorization, by the similarities subtest of the Wechsler Adult Intelligence Scale--Revised and the Wisconsin Card Sorting Test. Neuropsychological tests of motor and constructional functions were used as control tasks. The patients also underwent magnetic resonance imaging (MRI) studies in which new neuroimaging techniques were used to derive measurements of volume and three-dimensional surface renderings of temporal lobe structures. RESULTS: Spearman rank-order correlations indicated significant associations between poor scores on tests of verbal memory, abstraction, and categorization and reduced volume in temporal lobe structures, including the parahippocampal gyrus and posterior superior temporal gyrus (left and right). By contrast, performance on tests of visual memory and on control tasks was not correlated with MRI temporal lobe abnormalities. CONCLUSIONS: These findings suggest a significant but modest relation between reduced volume in specific temporal lobe regions and neuropsychological deficits in abstraction, categorization, and verbal memory, all of which may reflect a dysfunctional semantic system in schizophrenia.

Aberrant semantic activation in schizophrenia: a neurophysiological study.

OBJECTIVE: Schizophrenia has long been thought to be characterized by a fundamental disturbance in semantic associations, which has often been presumed to be of neurobiological origin. The authors examined the neurophysiological characteristics of semantic processing in schizophrenic patients. METHOD: During EEG recording, 15 schizophrenic patients and 15 age-matched comparison subjects read sentences that had either sensible or nonsensical endings. The authors recorded the N400 component, a specific negative event-related brain potential occurring approximately 400 msec after the final word in the sentence. N400 is highly, if not uniquely, sensitive to semantic expectancy and context, and larger, more negative N400 amplitude is associated with increased semantic unexpectancy. RESULTS: In relation to the normal comparison subjects, the schizophrenic patients demonstrated prolonged N400 latency after nonsensical sentence endings and also showed enhanced N400 negativity, regardless of the sense of the sentence ending. CONCLUSIONS: These findings suggest slower and more diffuse semantic activation in patients with schizophrenia, perhaps reflective of a disease-related failure to maintain and to use semantic context.

Can insulin therapy delay or prevent insulin-dependent diabetes mellitus?

Although the precise events preceding insulin-dependent diabetes mellitus (IDDM, type 1 diabetes) have not yet been elucidated, it is known that IDDM results from a slow, progressive, immune process directed against pancreatic islet beta cells. Disrupting this autoimmune process has been the focus of research aimed at preventing or slowing the disease progression. Technologic advances in predicting the onset and likelihood of developing IDDM have made it possible to study the effects of early immune intervention. The National Institutes of Health recently launched a large-scale, multicenter trial to evaluate the effectiveness of insulin as preventive therapy. Although many different immunosuppressive and immunomodulating agents have been investigated, the use of insulin as a prophylactic agent is a fairly recent concept. Several methods have been used to halt the autoimmune destruction of the pancreas, with animal and human studies serving as the basis for insulin in preventing IDDM.

Preparing women for the profession: a course using structured role-model analysis.

In response to increasing numbers of women entering pharmacy, a course was developed at the University of California, San Francisco, School of Pharmacy, addressing issues facing women in the profession. Our purpose was to prepare female students for their future careers by discussing career planning and management; the complexities of balancing career and family life; and career commitment. The technique of structured role-model analysis was used to encourage students to seek out, listen to, and learn from successful role-models. This technique enabled students to identify recurrent themes, advice and strategies among successful pharmacists who participated as guest speakers. Students were assisted in formulating their own career plans and developing a strategy for accomplishment. Courses of this type can increase a young woman's sophistication as she enters the profession and enable her to make more intelligent career decisions.

Practice patterns, attitudes and activities of Caucasian vs. Asian University of California-San Francisco PharmD graduates.

The results of a 1982 survey of graduates of the University of California at San Francisco (UCSF) doctor of pharmacy degree program were re-analyzed to explore whether cultural differences between Asian and Caucasian PharmD graduates affected professional practice patterns, attitudes and activities. Of the 732 respondents, 408 (56 percent) were Caucasians and 262 (36 percent) were Asians. Asian females had significantly fewer years of college education before entering pharmacy school and spend significantly fewer hours in the practice of pharmacy or related activities. Caucasians had a slightly higher grade point average than Asians. The mean score on the California State Board of Pharmacy Licensure Examination did not differ between the groups. For their first position following graduation, Asians predominated in operational positions, while Caucasians held clinical positions more frequently. Thirty-eight percent of Caucasians vs. 18 percent of Asians were taking or had completed postgraduate residency or fellowship training. An analysis of current jobs revealed that Asian males had the greatest increase in clinical positions when compared to the first position. Males of both ethnicities made the greatest gains in annual salary and in management positions compared to females.

Religion: friend or foe of the aging?

Religion can be a guide in the quest of older adults for a fuller understanding of their lives and purposes as they cope with the diminishments brought about by aging.

Meiosis and early cleavage in Drosophila melanogaster eggs: effects of the claret-non-disjunctional mutation.

The claret-non-disjunctional (cand) mutation is a female-specific mutation in Drosophila melanogaster, which causes a high frequency of mortality (89--90%) in eggs laid by the homozygous females. Among the progeny that survive to the adult stage, greater than 50% are aneuploid and/or mosaic for the X and number 4 chromosomes. The genetic studies of cand indicate that it is homologous to the claret mutation (ca-simulans) in Drosophila simulans. The cytological effect of the cand mutation on meiosis I and the early cleavage divisions has been observed at the light microscope level in stage 14 ovarian and fertilized uterine eggs, respectively. Four classes of metaphase I figures were observed. These include those with: (1) two or more spindles; (2) spindles that were abnormally wide and the bivalents widely separated; (3) unipolar spindles; and (4) apparently normal bipolar spindles. The three abnormal classes of metaphase I figures included 80% of the eggs examined at this stage. Among the cleavage stage eggs examined 69% showed highly abnormal mitotic figures, including multipolar spindles, and the nuclei in these eggs were found in clusters, rather than dispersed throughout the ooplasm. In addition to the cytological abnormalities observed, 17--23% of the eggs produced by the cand females showed morphological abnormalities. These abnormalities included eggs having three of four dorsal filaments, eggs that had a truncated shape, and abnormally small eggs. These abnormalities may not be an aspect of the cand syndrome, but they are due to recessive genes located on the third chromosome. Although the cand and ca-simulans mutations both affect the formation of the spindle apparatus during meiosis and the early cleavage divisions, the effects of these two mutations differ considerably in detail. The effect of the ca-simulans mutation appears to be more severe than the effect of cand. A model to explain the relationship between the effect of the cand mutation on meiosis I and the early cleavage divisions is presented, and evidence to support the model is discussed.

Heterogeneity of microtubule organizing center components as revealed by monoclonal antibodies to mammalian centrosomes and to nucleus-associated bodies from dictyostelium.

The molecular composition of two morphologically distinct microtubule-organizing centers (MTOCs) was compared by probing with monoclonal antibodies raised against (i) nucleus-associated bodies (NABs) isolated in a complex with nuclei from the cellular slime mold Dictyostelium discoideum and (ii) mammalian mitotic spindles isolated from Chinese hamster ovary (CHO) cells. The staining patterns observed by immunofluorescence microscopy in whole CHO cells and Dictyostelium amoebae showed that the distribution of thirteen MTOC antigens is heterogeneous. Not all antibodies recognized the MTOC in both interphase and mitosis. Most of the anti-MTOC antibodies cross-reacted with other cellular organelles such as nuclei, Golgi apparatus-like aggregates and cytoskeletal elements. Two antibodies, CHO3 and AX3, recognized phosphorylated epitopes present in both mammalian centrosomes and Dictyostelium NABs. On immunoblots, most of the antibodies showed multiple bands, often of high molecular weight, indicating that the antigenic determinants are shared among different molecules. One antibody inhibited the regrowth of microtubules onto centrosomes in vitro after addition of exogenous tubulin to detergent-lysed CHO cells on coverslips; this antibody binds to an antigen(s) that might be essential for the microtubule-nucleating activity of centrosomes. These observations demonstrate that molecular components in different MTOCs exhibit a variety of distinct subcellular localizations and functional properties, and that some antigenic molecules have been conserved among morphologically distinct MTOCs.

Identification of ubiquitous high-molecular-mass, heat-stable microtubule-associated proteins (MAPs) that are related to the Drosophila 205-kDa MAP but are not related to the mammalian MAP-4.

AX3, a monoclonal antibody raised against isolated microtubule-organizing centers of Dictyostelium discoideum, stains microtubule-containing structures in species ranging from Dictyostelium to human. On immunoblots, the AX3 antibody recognizes heat-stable proteins in the 260- to 280-kDa molecular-mass range in a number of different species. The AX3 antigens from HeLa and embryonic mouse fibroblast cells coprecipitate with microtubules in vitro, indicating that these antigens are, indeed, MAPs. The AX3 antigens are not immunologically related to the mammalian MAP-2 or MAP-4 but are related to the 205-kDa MAP of Drosophila. This report describes a structural-type MAP in Dictyostelium and a MAP that is detected in a wide variety of species. The Drosophila 205-kDa MAP had previously been proposed to represent a member of the MAP-4 class of proteins. From the results reported here, however, it is suggested that proteins recognized by AX3 monoclonal antibody, including the Drosophila 205-kDa MAP, represent a distinct class of MAPs that has been widely conserved through evolution.