The Removal of Viruses from Water by Conventional Water-Treatment Practices

The purpose of this investigation was to determine the effectiveness of conventional water-treatment methods in removing viruses from raw water sources. Those processes studied included alum flocculation, rapid sand filtration of fleeced and unflocced water samples, and chlorine disinfection. This study was approached using coliphage f2 as a seeded indicator of treatment efficiency. Coliphage f2 was chosen as an indicator because of its similarities to enteric viral pathogens in both morphology and sensitivity to water-treatment processes. Coliphage f2 was found to occur naturally in surface waters, but not in numbers sufficient to interfere with calculations. A sand filter for laboratory use was constructed with thin-walled PVC pipe, which was supported in a vertical position. Filter columns of 10-, 20-, and 30-inch depths were constructed either entirely of sand or as dual-media filters with a 1:2 ratio of sand to anthracite coal. Flow rate in the 30in column was adjusted to that reported for rapid sand filtration by adjusting the head of water above the filter bed. Duplicate one-liter samples of chlorinated final effluent were seeded with 10ml of an f2 stock (ca. 106pfu/ml). To one sample was added 0.12g alum and the mixture was stirred and allowed to settle. Phage titer of the supernatant was determined by the agar overlay method. The samples were then run through duplicate filters and the titers of the filtrates were determined. Resulting titers were compared to the original titer levels, and the efficiency of the processes were calculated as percent recovery. Turbidity was also measured on both samples before and after filtration. Alum flocculation followed by settling resulted in a wide range of reduction of the seeded f2. In most cases at least a one-log (90%) reduction was obtained and in several cases at least a two-log (99%) reduction occurred. The variability in phage reduction was attributed to the quality and quantity of floc produced. Filtration of unflocced, seeded water through sand and dual-media filters of various lengths resulted in generally low f2 removal. In only a few instances did such treatment result in a one-log (90%) reduction and in most cases the removal by filtration was negligible. Flocculation without settling, followed by filtration, removed significant numbers of the seeded f2. In several instances a three-log (99.9%) reduction occurred and generally a two-log (99%) reduction was observed. No correlation of f2 removal vs. column depth was observed. In addition, neither matrix was shown to remove f2 better than the other. The removal of turbidity by filtration roughly paralleled f2 removal. However, the large variations in turbidity and phage removal levels precludes the use of turbidity reductions as a satisfactory criterion for judging the efficiency of the process in removing viruses. Chlorine disinfection at 2ppm total residual chlorine resulted in an 80% reduction in f2 after a 2hr contact time; most of this reduction (68-79%) occurred within the first two minutes of chlorine contact, and corresponded with a rapid decrease in the free residual chlorine level. Further disinfection occurred throughout the 2hr contact time, but at a markedly slower rate. It was concluded that, connected in series in a water-treatment system, flocculation, filtration, and chlorination could be expected to reduce indigenous viral populations by at least 99.8-99.98%

Interacting Random Walkers and Non-Equilibrium Fluctuations

We introduce a model of interacting Random Walk, whose hopping amplitude depends on the number of walkers/particles on the link. The mesoscopic counterpart of such a microscopic dynamics is a diffusing system whose diffusivity depends on the particle density. A non-equilibrium stationary flux can be induced by suitable boundary conditions, and we show indeed that it is mesoscopically described by a Fourier equation with a density dependent diffusivity. A simple mean-field description predicts a critical diffusivity if the hopping amplitude vanishes for a certain walker density. Actually, we evidence that, even if the density equals this pseudo-critical value, the system does not present any criticality but only a dynamical slowing down. This property is confirmed by the fact that, in spite of interaction, the particle distribution at equilibrium is simply described in terms of a product of Poissonians. For mesoscopic systems with a stationary flux, a very effect of interaction among particles consists in the amplification of fluctuations, which is especially relevant close to the pseudo-critical density. This agrees with analogous results obtained for Ising models, clarifying that larger fluctuations are induced by the dynamical slowing down and not by a genuine criticality. The consistency of this amplification effect with altered coloured noise in time series is also proved.Comment: 8 pages, 7 figure

Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes

Grupo de trabajo: The Genographic Consortium.[Background] The analysis of human Y-chromosome variation in the context of population genetics and forensics requires the genotyping of dozens to hundreds of selected single-nucleotide polymorphisms (SNPs). In the present study, we developed a 121-plex (121 SNPs in a single array) TaqMan array capable of distinguishing most haplogroups and subhaplogroups on the Y-chromosome human phylogeny in Europe.[Results] We present data from 264 samples from several European areas and ethnic groups. The array developed in this study shows >99% accuracy of assignation to the Y human phylogeny (with an average call rate of genotypes >96%).[Conclusions] We have created and evaluated a robust and accurate Y-chromosome multiplex which minimises the possible errors due to mixup when typing the same sample in several independent reactions.Peer reviewe

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

Changes In Rural Affinity Among Rural Medical Students As They Experience Education In An Urb

Abstract Introduction The maldistribution of physicians in the United States has led to a shortage of healthcare providers in rural areas and rural patients being underserved. A physician’s connections to rural settings, including upbringing and medical training, often influence the decision to practice in rural areas. This study examines opinions from medical students who participated in a regional rural campus track, which includes summer immersion programs, rural-focused sessions, and clinical rotations. The authors hypothesized that Rural Track students experience urban disruption, and their opinions about rural living and practice would become increasingly less positive over time while students lived at the urban campus for preclinical coursework. Materials and Methods The Rural Health Opinion Survey (RHOS), a previously published measure of opinions concerning living and practicing in rural areas, was administered to students at one public medical school located in Louisville, Kentucky. Factor analysis was performed on each of the three sections of the survey (items related to rural living, patients in rural areas, and physicians in rural areas), and composite subscale scores were calculated for each student. The first phase of this large longitudinal study reported here uses t-tests to compare pre- and post-test scores for 36 students in the Rural Track program. Scores of M1/M2 students who were based at the urban campus were also compared to M3/M4 students who had returned to the rural campus. Results Ninety-two percent (36/39) of Rural Track students completed both pre- and post-surveys, and of these respondents, 89% percent (32/36) grew up in a hometown with fewer than 30,000 people. Overall scores were not significantly different between Rural Track M1/M2 in the urban setting and the Rural Track M3/M4 students based at the rural campus. M3/M4 students showed a differential positive opinion over time of rural comfortable living that approached significance and agreed less that the rural physician workload is heavier. M1/M2 students expressed more positive opinions over time about availability of quality service. Both groups showed strong agreement over time that rural patients are more motivated. Discussion Our hypothesis that Rural Track students on the urban campus would show increasingly less positive opinions about rural health and practice was not supported. Students may not have experienced urban disruption because of the Rural Track curriculum elements, and/or time in the urban environment may have reinforced rural affinity by providing new perspective on the positive aspects of rural settings. Further research and efforts are necessary to identify critical points of reconnection for medical students and to support rural affinity within medical school curriculum. Upcoming research efforts will address the overall hypothesis that Rural Track students’ continued connection to rural settings generates more positive opinions about rural living and practice as compared to opinions from students with rural backgrounds who spend all four years of medical school in the urban setting

Wirkungen naturwissenschaftlicher Bildungsangebote auf pädagogische Fachkräfte und Kinder

Die Autorinnen und Autoren untersuchten die Wirkungen naturwissenschaftlicher Bildungsangebote auf die kognitiven und motivationalen Kompetenzen von pädagogischen Fachkräften und Kindern in Kitas. Insgesamt konnte aufgezeigt werden, dass die Teilnahme an naturwissenschaftlichen Fortbildungen in einem positiven Zusammenhang mit den naturwissenschaftlichen professionellen Kompetenzen pädagogischer Fachkräfte steht und dass Kinder aus Einrichtungen mit einem expliziten naturwissenschaftlichen Schwerpunkt höhere Lernfreude und höheres Selbstvertrauen in Bezug auf Naturwissenschaften zeigen als Kinder in Einrichtungen ohne naturwissenschaftlichen Schwerpunkt. Sie untersuchten zudem die Interaktionsqualität und mögliche sprachliche Bildungswirkungen im Kontext naturwissenschaftlicher Bildungsangebote bei Vorschulkindern. Die Studie legt nahe, dass naturwissenschaftliche Fortbildungen die naturwissenschaftlichen Kompetenzen wie auch den Spracherwerb der Kinder unterstützen und die Prozessqualität der Fachkräfte in naturwissenschaftsbezogenen Situationen bestimmen können. Das Schlusskapitel des Bandes beschreibt die Umsetzung der wissenschaftlichen Empfehlungen in den inhaltlichen Angeboten der Stiftung „Haus der kleinen Forscher“ und ihrer fachlichen Weiterentwicklung. (DIPF/Orig.

The GenoChip: A New Tool for Genetic Anthropology

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project’s new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. TheGenoChip includes ancestry informativemarkers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all knownY-chromosome andmtDNAhaplogroups. The chip was carefully vetted to avoid inclusion ofmedically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highestmean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPswithout any known health,medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics

Geographic population structure analysis of worldwide human populations infers their biogeographical origins

The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing

A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems

Xanthomonas oryzae (Xo) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae (Xcl), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra, and is a close relative of Xo. L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo. Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl. Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae (Xol) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems