Trends in Summer Chemistry Linked to Productivity in Lakes Recovering from Acid Deposition in the Adirondack Region of New York

The US Environmental Protection Agency established the Adirondack Effects Assessment Program (AEAP) to evaluate and monitor the status of biological communities in lakes in the Adirondack region of New York that have been adversely affected by acid deposition. This program includes chemical analysis of 30 lakes, sampled two to three times each summer. Results of trends analysis for lake chemistry and chlorophyll a (chlor a) are presented for 1994 to 2003, and a general comparison is made with recent results of the Adirondack Long-Term Monitoring (ALTM) Program, which included chemical analysis of all but two of these lakes (plus an additional 24 lakes) monthly, year-round for 1992–2004. Increases in pH were found in 25 of the 30 AEAP lakes (P < 0.05) and increases in acid-neutralizing capacity (ANC) were found in 12 of the 30 lakes (P < 0.05). Concentrations of both SO ₄ ²⁻ and Mg²⁺ decreased in 11 lakes (P < 0.05), whereas concentrations of NO ₃ ⁻ decreased in 20 lakes (P < 0.05). Concentrations of NH ₄ ⁺ decreased in 10 lakes at a significance level of P < 0.05 and in three other lakes based on P < 0.1. Concentrations of inorganic and organic monomeric aluminum generally were below the reporting limit of 1.5 μmol L⁻¹, but decreases were detected in four and five lakes, respectively (P < 0.1). Concentrations of chlor a increased in seven lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. A significant inverse correlation was also found between chlor a and NO ₃ ⁻ concentrations in nine lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. Results of AEAP analysis of lake chemistry were similar to those of the ALTM Program, although decreases in SO ₄ ²⁻ concentrations were more evident in the year-round ALTM record. Overall, the results suggest (a) a degree of chemical recovery from acidification during the summer, (b) an increase in phytoplankton productivity, and (c) a decreasing trend in NO ₃ ⁻ concentrations resulting from the increased productivity.     

Global Analysis of Rice Tungro Spherical Virus Coat Proteins Reveals New Roles in Evolutionary Consequences

Rice tungro disease is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). RTSV has a capsid comprising three coat proteins (CP) species. Three CP genes of RTSV-AP isolate were sequenced and compared with 9 other isolates reported worldwide for their phylogenetic survey of recombination events which revealed that in general Indian isolates are forming one separate cluster while those of Philippines and Malaysia forming a different cluster. A significant proportion of recombination sites were found in the CP1 gene, followed by CP2 and CP3 suggesting that it is a major phenomenon in the evolution of various isolates of RTSV. Some interesting domains and motifs such as; 3,4-dihydroxy-2-butanone 4-phosphate synthase in CP1, Type 1 glutamine amidotransferase domain and RNA binding motifs in CP2, domains of receptor proteins in CP3, and glycosylation motif in CP2 and CP3 were also obtained in RTSV coat protein. In addition, simple modular architecture research tool (SMART) analysis of coat proteins of RTSV predicted the coat protein domain of calicivirus suggesting evolutionary linkages between plant and animal viruses. This study provides an opportunity to establish the molecular evolution and sequence-function relationship of RTSV.     

Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old

Vertebrate genomic assemblies were analyzed for endogenous sequences related to any known viruses with single-stranded DNA genomes. Numerous high-confidence examples related to the Circoviridae and two genera in the family Parvoviridae, the parvoviruses and dependoviruses, were found and were broadly distributed among 31 of the 49 vertebrate species tested. Our analyses indicate that the ages of both virus families may exceed 40 to 50 million years. Shared features of the replication strategies of these viruses may explain the high incidence of the integrations.It has long been appreciated that retroviruses can contribute significantly to the genetic makeup of host organisms. Genes related to certain other viruses with single-stranded RNA genomes, formerly considered to be most unlikely candidates for such contribution, have recently been detected throughout the vertebrate phylogenetic tree (1, 6, 13). Here, we report that viruses with single-stranded DNA (ssDNA) genomes have also contributed to the genetic makeup of many organisms, stretching back as far as the Paleocene period and possibly the late Cretaceous period of evolution.Determining the evolutionary ages of viruses can be problematic, as their mutation rates may be high and their replication may be rapid but also sporadic. To establish a lower age limit for currently circulating ssDNA viruses, we analyzed 49 published vertebrate genomic assemblies for the presence of sequences derived from the NCBI RefSeq database of 2,382 proteins from known viruses in this category, representing a total of 23 classified genera from 7 virus families. Our survey uncovered numerous high-confidence examples of endogenous sequences related to the Circoviridae and to two genera in the family Parvoviridae: the parvoviruses and dependoviruses (Fig. ​(Fig.11).Open in a separate windowFIG. 1.Phylogenetic tree of vertebrate organisms and history of ssDNA virus integrations. Times of integration of ancestral dependoviruses (yellow icosahedrons), parvoviruses (blue icosahedrons), and circoviruses (triangles) are approximate.The Dependovirus and Parvovirus genomes are typically 4 to 6 kb in length, include 2 major open reading frames (encoding replicase proteins [Rep and NS1, respectively] and capsid proteins [Cap and VP1, respectively]), and have characteristic hairpin structures at both ends (Fig. ​(Fig.2).2). For replication, these viruses depend on host enzymes that are recruited by the viral replicase proteins to the hairpin regions, where self-primed viral DNA synthesis is initiated (2). Circovirus genomes are typically ∼2-kb circles. DNA of the type species, porcine circovirus 1 (PCV-1), contains a stem-loop structure within the origin of replication (Fig. ​(Fig.2),2), and the largest open reading frame includes sequences that are homologous to the Parvovirus replicase open reading frame (9, 11). The circoviruses also depend on host enzymes for replication, and DNA synthesis is self-primed from a 3′-OH end formed by endonucleolytic cleavage of the stem-loop structure (4). The frequency of Dependovirus infection is estimated to be as high as 90% within an individual''s lifetime. None of the dependoviruses have been associated with human disease, but related viruses in the family Parvoviridae (e.g., erythrovirus B19 and possibly human bocavirus) are pathogenic for humans, and members of both the Parvoviridae and the Circoviridae can cause a variety of animal diseases (2, 4).Open in a separate windowFIG. 2.Schematics illustrating the structure and organization of Parvoviridae and Circoviridae genomes and origins of several of the longest-integrated ancestral viral sequences found in vertebrates. Integrations were aligned to the Dependovirus adeno-associated virus 2 (AAV2), the Parvovirus minute virus of mice (MVM), and the Circovirus porcine circovirus 1 (PCV-1). The inverted terminal repeat (ITR) sequences in the Dependovirus and Parvovirus genomes are depicted on an expanded scale. A linear representation of the circular genome of PCV-1 is shown with the 10-bp stem-loop structure on an expanded scale. Horizontal lines beneath the maps indicate the lengths of similar sequences that could be identified by BLAST. The numbers indicate the locations of amino acids in the viral proteins where the sequence similarities in the endogenous insertions start and end. The actual ancestral virus-derived integrated sequences may extend beyond the indicated regions.With some ancestral endogenous sequences that we identified, phylogenetic comparisons can be used to estimate age. For example, as a Dependovirus-like sequence is present at the same location in the genomes of mice and rats, the ancestral virus must have existed before their divergence, more than 20 million years ago. Some Circovirus- and Dependovirus-related integrations also predate the split between dog and panda, about 42 million years ago. However, in most other cases, we rely on an indirect method for estimating age (1). As genomic sequences evolve, they accumulate new stop codons and insertion/deletion-induced frameshifts. The rates of these events can be tied directly to the rates of neutral sequence drift and, therefore, the time of evolution. To apply this method, we first performed a BLAST search of vertebrate genomes for all known ssDNA virus proteins (BLAST options, -p tblastn -M BLOSUM62 -e 1e−4). Candidate sequences were then recorded, along with 5 kb of flanking regions, and then again aligned against the database of ssDNA viruses to find the most complete alignment (BLAST options, -t blastx -F F -w 15 -t 1500 -Z 150 -G 13 -E 1 -e 1e−2). Detected alignments were then compared with a neutral model of genome evolution, as described in the supplemental material, and the numbers of stop codons and frameshifts were converted into the expected genomic drift undergone by the sequences. The age of integration was then estimated from the known phylogeny of vertebrates (7, 10). Using these methods, we discovered that as many as 110 ssDNA virus-related sequences have been integrated into the 49 vertebrate genomes considered, during a time period ranging from the present to over 40 to 60 million years ago (Table ​(Table1;1; see also Tables S1 to S3 in the supplemental material).

TABLE 1.

Selected endogenous sequences in vertebrate genomes related to single-stranded DNA viruses

High Genetic Diversity of Newcastle Disease Virus in Wild and Domestic Birds in Northeastern China from 2013 to 2015 Reveals Potential Epidemic Trends

Newcastle disease (ND), caused by the virulent Newcastle disease virus (NDV), is one of the most important viral diseases of birds globally, but little is currently known regarding enzootic trends of NDV in northeastern China, especially for class I viruses. Thus, we performed a surveillance study for NDV in northeastern China from 2013 to 2015. A total 755 samples from wild and domestic birds in wetlands and live bird markets (LBMs) were collected, and 10 isolates of NDV were identified. Genetic and phylogenetic analyses showed that five isolates from LBMs belong to class I subgenotype 1b, two (one from wild birds and one from LBMs) belong to the vaccine-like class II genotype II, and three (all from wild birds) belong to class II subgenotype Ib. Interestingly, the five class I isolates had epidemiological connections with viruses from southern, eastern, and southeastern China. Our findings, together with recent prevalence trends of class I and virulent class II NDV in China, suggest possible virus transmission between wild and domestic birds and the potential for an NDV epidemic in the future.     

Two New Species of Interstitial Marine Triclads from the North American Pacific Coast, with Comments on Evolutionary Trends and Systematics in Tricladida (Turbellaria)

Holmquist, Ch. and Karling, T. G. (Section of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden.) Two new species of marine triclads from the North American Pacific coast, with comments on evolutionary trends and systematics in Tricladida (Turbellaria). Zool. Scripta 1(3–4): 175–184, 1972.–Two marine triclads, Oregoniplana opisthopora gen. et sp.n. and Pacificides psammophilus gen. et sp.n. are described from the Pacific coast of USA. They are inhabitants of sand in the surf zone. They are provisionally included in the family Procerodidae but their anatomy is aberrant in several respects; they elucidate some evolutionary trends as well as some unsatisfactory points in the systematics of the aquatic triclads.     

Age-Related Mortality Trends in Italy from 1901 to 2008

We stratified the Italian population according to age and gender in order to evaluate mortality trends over more than one century. Data covering the 1901–2008 period were used to study the yearly variations in mortality. Fluctuations in age-adjusted mortality curves were analyzed by Join Point Regression Models, identifying Join Points and Annual Percent Changes. A consistent decline in all-cause mortality occurred across the whole period, the most striking variations being observed in the 0–49 years population. In 1901, other and undefined diseases were the main causes of death, followed by infectious, digestive, and respiratory diseases in the 0–49 years population and by respiratory, cardiovascular, and cerebrovascular diseases in the ≥50 years population groups. In 2008 the main causes of death were accidents (males) and tumors (females) in the 0–49 age class, tumors in the 50–69 age class (both genders), and tumors (males) and cardiovascular diseases (females) in the elderly. The results highlight the interplay between age and gender in affecting mortality trends and reflect the dramatic progress in nutritional, lifestyle, socioeconomic, medical, and hygienic conditions.     

Resveratrol and the Pharmacology of Aging: A New Vertebrate Model to Validate an Old Molecule

The natural phytoalexin resveratrol, found in grapes and red wine, recently raised to public fame for its positive effects on longevity in yeasts, worms and flies. Resveratrol anti-cancer and anti-inflammatory in vitro action on mammalian cell cultures also suggest a possible positive effect on human health and life-expectancy. To study the effects of resveratrol on vertebrate aging is obviously a particularly relevant question. We have studied resveratrol effects in a very short-lived vertebrate: the annual fish Nothobranchius furzeri. Resveratrol treatment prolonged lifespan and delayed the onset of age-related dysfunctions in this fish. This result identifies resveratrol as the first molecule which consistently retards aging in organisms as diverse as yeast, worm, fly and fish, but it also reveals the potential of this short-lived fish as an animal model for pharmacological research. Moreover, being related to stickleback (Gasterosteus aculeatus) the “pufferfishes” Takifugu and Tetraodon, and even more closely related to medaka (Oryzias latipes), it can greatly beneficiate from the recent development of genomic resources for these fish models and in the future become a complete model system for the aging research community.     

Occupational Noise Annoyance Linked to Depressive Symptoms and Suicidal Ideation: A Result from Nationwide Survey of Korea

Background

Noise, or undesirable sound, is one of the most common environmental stressors, and it can cause various health effects. Beyond the auditory consequences of occupational noise exposure, extra-auditory effects such as psychological problems have also been found. The aim of the current study is to elucidate the association between occupational noise annoyance and psychological symptoms, including symptoms of depression and suicidal ideation.

Methods

A total of 10,020 participants (5,410 men and 4,610 women) were included in the current analysis, using data from the fourth Korean National Health and Nutrition Examination Survey (KNHANES). Self-report questionnaires were used to assess noise annoyance levels, depressive symptoms, and suicidal ideation. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for psychosocial symptoms were calculated using multiple logistic regression models.

Results

Compared to the no noise annoyance group, ORs (95% CI) of the severe annoyance groups were 1.58 (1.12–2.23) and 1.76 (1.29–2.40) in men and 1.49 (1.05–2.11) and 1.41 (1.01–1.97) in women for depressive symptoms and suicidal ideation, respectively. The ORs (95% CI) for severe noise annoyance in those with less than five hours of sleep were 2.95 (1.46–5.96) and 2.05 (1.01–4.16) in men and women, respectively, compared with those with no noise annoyance and a sleep time of more than five hours.

Conclusion

Our study shows that occupational noise annoyance is significantly related to mental health, including depressive symptoms and suicidal ideation after controlling for individual and socio-demographic characteristics even with gender stratification. However, prospective studies with quantified noise exposure assessment were needed to elucidate the causality on the association between noise annoyance and psychological symptoms.     

Trends in large-scale mouse mutagenesis: from genetics to functional genomics

The primary goal of mouse mutagenesis programmes is to develop a fundamental research infrastructure for mammalian functional genomics and to produce human disease models. Many large-scale programmes have been ongoing since 1997; these culminated in the International Knockout Mouse Consortium (IKMC) in 2007 with the aim to establish knockout and conditional mouse strains for all mouse genes. This article traces the origins and rationale of these large-scale mouse mutagenesis programmes.     

Child Deaths Due to Injury in the Four UK Countries: A Time Trends Study from 1980 to 2010

Background

Injuries are an increasingly important cause of death in children worldwide, yet injury mortality is highly preventable. Determining patterns and trends in child injury mortality can identify groups at particularly high risk. We compare trends in child deaths due to injury in four UK countries, between 1980 and 2010.

Methods

We obtained information from death certificates on all deaths occurring between 1980 and 2010 in children aged 28 days to 18 years and resident in England, Scotland, Wales or Northern Ireland. Injury deaths were defined by an external cause code recorded as the underlying cause of death. Injury mortality rates were analysed by type of injury, country of residence, age group, sex and time period.

Results

Child mortality due to injury has declined in all countries of the UK. England consistently experienced the lowest mortality rate throughout the study period. For children aged 10 to 18 years, differences between countries in mortality rates increased during the study period. Inter-country differences were largest for boys aged 10 to 18 years with mortality rate ratios of 1.38 (95% confidence interval 1.16, 1.64) for Wales, 1.68 (1.48, 1.91) for Scotland and 1.81 (1.50, 2.18) for Northern Ireland compared with England (the baseline) in 2006–10. The decline in mortality due to injury was accounted for by a decline in unintentional injuries. For older children, no declines were observed for deaths caused by self-harm, by assault or from undetermined intent in any UK country.

Conclusion

Whilst child deaths from injury have declined in all four UK countries, substantial differences in mortality rates remain between countries, particularly for older boys. This group stands to gain most from policy interventions to reduce deaths from injury in children.     

Trends in Overweight and Obesity among Children and Adolescents in China from 1981 to 2010: A Meta-Analysis

Background

Overweight/obesity is a serious public health problem that affects a large part of the world population across all age and racial/ethnic groups. However, there has not been a meta-analysis of the prevalence of childhood and adolescent overweight/obesity in China during the past 30 years.

Methods

The China National Knowledge Infrastructure and Wanfang DATA, MEDLINE, EMBASE and Cumulative Index to Nursing and Allied Health Literature were searched for relevant studies published between January 1970 and June 2012. The prevalence of overweight/obesity over time was pooled using Stata/SE, version 9. Summary statistics (odds ratios, ORs) were used to compare sex-specific and urban-rural preponderance of overweight/obesity using Review Manager.

Results

After screening 1326 papers, we included 35 papers (41 studies), most of medium quality. The prevalence of overweight/obesity increased from 1.8% (95% confidence interval [CI], 0.4%–3.1%) and 0.4% (95% CI, −0.1% to −0.8%) respectively in 1981–1985 to 13.1% (95% CI, 11.2%–15.0%) and 7.5% (95% CI, 6.6%–8.4%) respectively in 2006–2010. The average annual increase was 8.3% and 12.4% respectively. Boys were more likely to be overweight/obese than girls (OR, 1.36; 95% CI, 1.24–1.49 and OR, 1.68; 95% CI, 1.52–1.86 respectively). The prevalence of overweight/obesity was higher in urban areas than in rural areas (OR, 1.66; 95% CI, 1.54–1.79 and OR, 1.97; 95% CI, 1.68–2.30 respectively). For age-specific subgroup analyses, both overweight and obesity increased more rapidly in the toddler stage than in other developmental stages. Sensitivity analyses showed that sample-size differences, study quality, overweight/obesity criteria and geographical distribution affected overweight/obesity prevalence.

Conclusions

Toddlers and urban boys were at particularly high risk; the prevalence in these groups increased more rapidly than in their counterparts. Public health prevention strategies are urgently needed to modify health behaviors of children and adolescents and control overweight/obesity in China.