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%

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

Population differentiation of Southern Indian male lineages correlates with agricultural expansions predating the caste system

Christina J. Adler, Alan Cooper, Clio S.I. Der Sarkissian and Wolfgang Haak are contributors to the Genographic ConsortiumPrevious studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed, <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna(caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.GaneshPrasad ArunKumar, David F. Soria-Hernanz, Valampuri John Kavitha, Varatharajan Santhakumari Arun, Adhikarla Syama, Kumaran Samy Ashokan, Kavandanpatti Thangaraj Gandhirajan, Koothapuli Vijayakumar, Muthuswamy Narayanan, Mariakuttikan Jayalakshmi, Janet S. Ziegle, Ajay K. Royyuru, Laxmi Parida, R. Spencer Wells, Colin Renfrew, Theodore G. Schurr, Chris Tyler Smith, Daniel E. Platt, Ramasamy Pitchappan, The Genographic Consortiu

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%

A second-generation combined linkage–physical map of the human genome

We have completed a second-generation linkage map that incorporates sequence-based positional information. This new map, the Rutgers Map v.2, includes 28,121 polymorphic markers with physical positions corroborated by recombination-based data. Sex-averaged and sex-specific linkage map distances, along with confidence intervals, have been estimated for all map intervals. In addition, a regression-based smoothed map is provided that facilitates interpolation of positions of unmapped markers on this map. With nearly twice as many markers as our first-generation map, the Rutgers Map continues to be a unique and comprehensive resource for obtaining genetic map information for large sets of polymorphic markers

A Comprehensive Linkage Map of the Dog Genome

We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with ∼3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with ∼1500 loci. An additional ∼1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from ∼22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map