Widespread Co-occurrence Research Articles

Diversity, abundance, and persistence of antibiotic resistance genes in various types of animal manure following industrial composting

Aerobic composting is used widely for animal manure recycling, and it may reduce the amount of antibiotic resistance genes (ARGs) that enter the environment. We sampled three types of animal (bovine, chicken, and pig) manure and the corresponding composts from 12 large-scale farms, and tested multiple ARGs and mobile genetic elements (MGEs) by high-throughput qPCR. A total of 109 ARGs were detected in the manure and compost samples, thereby demonstrating that both are important ARG reservoirs. The diversity and abundance of ARGs were significantly higher in chicken and pig manure than bovine manure, but industrial composting was more efficient at reducing the ARGs in chicken manure than pig and bovine manure. Composting universally reduced some ARGs, but inconsistently influenced other ARGs from different types of animal manures. Network analysis detected the widespread co-occurrence of ARGs and MGEs. floR, ermF, catB3, aac(6′)-lb(akaaacA4), and aadA were identified as suitable indicator genes for estimating the total abundance of ARGs. Our results suggest that different animal species had significant effects on the diversity, abundance, and persistence of ARGs, where the abundance of transposons, heavy metal concentration, total nitrogen level, and the dosage and duration of exposure to antibiotics may explain these differences.

Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia.

Mitochondrial genome heteroplasmy-the presence of more than one genomic variant in individuals-is considered only occasional in animals, and most often involves molecules differing only by a few recent mutations. Thanks to new sequencing technologies, a large number of DNA fragments from a single individual can now be sequenced and visualized separately, allowing new insights into intra-individual mitochondrial genome variation. Here, we report evidence from both (i) massive parallel sequencing (MPS) of genomic extracts and (ii) Sanger sequencing of PCR products, for the widespread co-occurrence of two distantly related (greater than 1% nucleotide divergence, excluding the control region) mitochondrial genomes in individuals of a natural population of the leaf beetle Gonioctena intermedia Sanger sequencing of PCR products using universal primers previously failed to identify heteroplasmy in this population. Its occurrence was detected with MPS data and may have important implications for evolutionary studies. It suggests the need to re-evaluate, using MPS techniques, the proportion of animal species displaying heteroplasmy.

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.

In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration probabilities across tumors. We present Discrete Independence Statistic Controlling for Observations with Varying Event Rates (DISCOVER), a novel test that is more sensitive than other methods and controls its false positive rate. A pan-cancer analysis using DISCOVER finds no evidence for widespread co-occurrence, and most co-occurrences previously detected do not exceed expectation by chance. Many mutual exclusivities are identified involving well-known genes related to cell cycle and growth factor signaling, as well as lesser known regulators of Hedgehog signaling.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1114-x) contains supplementary material, which is available to authorized users.

Asian pheretimoid earthworms in North America north of Mexico: An illustrated key to the genera Amynthas, Metaphire, Pithemera, and Polypheretima (Clitellata: Megascolecidae).

The invasion of the pheretimoid earthworms in North America, especially the genera Amynthas and Metaphire, has raised increasing concerns among ecologists and land managers, in turn increasing the need for proper identification. However, the commonly used keys to this group are more than 30 years old with outdated taxonomic information and are based primarily on internal morphology. The requirement of significant amount of taxonomic expertise and dissection, even from the first entry of the key, has prevented broader use of these keys. As a result, many publications in the United States have used Amynthas spp. to represent the group without identifying the species. We present here a new key and diagnoses for the 16 pheretimoid earthworm species recorded in North America north of Mexico, including four genera: Amynthas (10), Metaphire (4), Pithemera (1), and Polypheretima (1). The descriptions were based on published records with modifications following inspection of specimens archived at the National Museum of Natural History, Smithsonian Institution, Washington, D.C. Photos of external and internal characters, including male pores, spermathecal pores, genital markings, spermathecae, prostate glands, and intestinal caeca, are presented to help identification. A summary of current knowledge about the ecology and historical context is provided for each species. We also highlight the previously overlooked and potentially common and widespread co-occurrence of three species-A. agrestis, A. tokioensis, and M. hilgendorfi-and point out that many recent claims of invasion of A. agrestis need to be re-evaluated for potential misidentification.

Good neighbours shaped by vigorous currents: Cold-water coral mounds and contourites in the North Atlantic

Over the recent years, two research fields addressing continental slope sedimentary systems have gained significant momentum: contourites and cold-water coral mounds. Being both related to intense bottom currents and being both dependent on sediment supply, they share some commonalities resulting in their widespread co-occurrence. However, as cold-water coral mounds predominantly occur in shallow to intermediate water depths, this co-occurrence is restricted to these depth levels. For both systems, the available knowledge is derived basically from North Atlantic Ocean settings, indicating the potential to discover such systems hidden in the other ocean basins (as well as still hidden in the Atlantic). Contourites and cold-water coral mounds have the capability of providing high-resolution palaeo-environmental records, although with often differing temporal ranges and/or temporal resolutions. Applying the concept of a joint exploitation of sedimentary records obtained from mounds and contourites offers the unique possibility of analysing contourite and mound development as well as the related palaeo-environmental settings much more comprehensively than done when only considering one of these archives. Thus, after two decades of intense research, providing significant knowledge about contourites and cold-water coral mounds from the North Atlantic, new ideas and concepts may arise from a close collaboration of scientists working in these two fields.

Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors.

RNA ligases have essential roles in many cellular processes in eukaryotes, archaea and bacteria, including in RNA repair and stress-induced splicing of messenger RNA. In archaea and eukaryotes, RNA ligases also have a role in transfer RNA splicing to generate functional tRNAs required for protein synthesis. We recently identified the human tRNA splicing ligase, a multimeric protein complex with RTCB (also known as HSPC117, C22orf28, FAAP and D10Wsu52e) as the essential subunit. The functions of the additional complex components ASW (also known as C2orf49), CGI-99 (also known as C14orf166), FAM98B and the DEAD-box helicase DDX1 in the context of RNA ligation have remained unclear. Taking advantage of clusters of eukaryotic orthologous groups, here we find that archease (ARCH; also known as ZBTB8OS), a protein of unknown function, is required for full activity of the human tRNA ligase complex and, in cooperation with DDX1, facilitates the formation of an RTCB-guanylate intermediate central to mammalian RNA ligation. Our findings define a role for DDX1 in the context of the human tRNA ligase complex and suggest that the widespread co-occurrence of archease and RtcB proteins implies evolutionary conservation of their functional interplay.

Co-occurrence of psychotic experiences and common mental health conditions across four racially and ethnically diverse population samples.

Prior research with racially/ethnically homogeneous samples has demonstrated widespread co-occurrence of psychotic experiences (PEs) and common mental health conditions, particularly multi-morbidity, suggesting that psychosis may be related to the overall severity of psychiatric disorder rather than any specific subtype. In this study we aimed to examine whether PEs are associated with the presence of specific disorders or multi-morbidity of co-occurring disorders across four large racially/ethnically diverse samples of adults in the USA. Data were drawn from the National Comorbidity Survey Replication (NCS-R), the National Survey of American Life (NSAL) and separately from the Asian and Latino subsamples of the National Latino and Asian American Study (NLAAS). Logistic regression models were used to examine the relationship between PEs and individual subtypes of DSM-IV disorder, and to test for a linear dose-response relationship between the number of subtypes and PEs. Prevalence of PEs was moderately greater among individuals with each subtype of disorder in each data set [odds ratios (ORs) 1.8-3.8], although associations were only variably significant when controlling for clinical and demographic variables. However, the sum of disorder subtypes was related to odds for PEs in a linear dose-response fashion across all four samples. PEs are related primarily to the extent or severity of psychiatric illness, as indicated by the presence of multiple psychiatric disorders, rather than to any particular subtype of disorder in these data. This relationship applies to the general population and across diverse racial/ethnic groups.

EARLY LADINIAN RADIOLARIAN FAUNA FROM THE MONTE SAN GIORGIO (SOUTHERN ALPS, SWITZERLAND): SYSTEMATICS, BIOSTRATIGRAPHY AND PALEO(BIO)GEOGRAPHIC IMPLICATIONS

A well-preserved radiolarian fauna was recovered from the lower part of the San Giorgio Dolomite (Monte San Giorgio, UNESCO WHL, Switzerland), belonging to the Eoprotrachyceras curionii Ammonoid Zone (earliest Ladinian). The depositional environment, consisting of an intraplatform basin with restricted circulation, seemingly resulted in an unusual radiolarian assemblage displaying neglegible percentages and very low diversity of Nassellaria. Seventy-three species have been identified and seven new species have been described: Eptingium danieli n. sp., Eptingium neriae n. sp., Parentactinosphaera eoladinica n. sp., Sepsagon ticinensis n. sp., Sepsagon ? valporinae n. sp., Novamuria wirzi n. sp. and Pessagnollum hexaspinosum n. sp. The taxonomic status of the recovered species has been reassessed and four new genera have been introduced: Bernoulliella gen. n., Eohexastylus gen. n., Ticinosphaera gen. n. and Lahmosphaera gen. n. The new radiolarian assemblages, the first so far described from the Monte San Giorgio, supplement further information to the taxa occurring in the uppermost Ladinocampe multiperforata Radiolarian Zone, as yet poorly defined, also confirming the absence of major changes in the radiolarian fauna across the Anisian/Ladinian boundary. The widespread co-occurrence of taxa doubtlessly testifies to the existence, in early Ladinian times, of open-marine connections between the basin of the Monte San Giorgio and the pelagic “Buchenstein” basins of the central and eastern South-Alpine domain and farther afield across the Tethys.

Widespread Co-occurrence of Virulent Pathogens Within California Amphibian Communities

The chytrid fungus Batrachochytrium dendrobatidis, ranaviruses, and trematodes (Ribeiroia ondatrae and echinostomes) are highly virulent pathogens known to infect amphibians, yet the extent to which they co-occur within amphibian communities remains poorly understood. Using field surveillance of 85 wetlands in the East Bay region of California, USA, we found that 68% of wetlands had ≥2 pathogens and 36% had ≥3 pathogens. Wetlands with high pathogen species richness also tended to cluster spatially. Our results underscore the need for greater integration of multiple pathogens and their interactions into amphibian disease research and conservation efforts.

Widespread co-occurrence of divergent mitochondrial haplotype lineages in a Central American species of poison frog (Oophaga pumilio)

Aim To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers. Location Costa Rica and Panama. Methods Sequence analyses of a mitochondrial (cytochrome b) and a nuclear (RAG-1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei. Results Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co-occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the ‘southern lineage’ shifted this barrier towards the north. Main conclusions Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus.

The prevalence and characteristics of back pain among school children in New Zealand

A cross-sectional survey among 245 children was conducted to establish the prevalence and characteristics of back pain in school children aged 11–14 years. A self-complete questionnaire was used to ascertain demographic details, pain prevalence, psychosocial parameters, school and leisure activities and family characteristics. In the last month, 58% of children had experienced spinal pain. In total, 31% of children reported that pain occurred in one part of the back, while 28% stated that pain presented in more than one spinal region. Pain in the last month was found to be equally prevalent in the low back (35%) and neck (36%) regions. Low back pain was associated with the most severe pain and pain lasting for the longest duration when compared with the upper back and neck regions. Further research should be directed towards investigating pain in the neck region and understanding the characteristics of symptom co-occurrence. Statement of Relevance:A survey was conducted to establish the prevalence and characteristics of back pain in school children. The results provide additional evidence that back pain is a serious problem in children aged 11–14 years, whilst also indicating widespread co-occurrence of pain in the neck, upper back and lower back spinal regions.

Chemical-genomic dissection of the CTD code

SummarySequential modifications of the RNA polymerase II (Pol II) carboxyl-terminal domain (CTD) coordinate the stage-specific association and release of cellular machines during transcription. Here we examine the genome-wide distributions of the “early” (phospho-serine 5), “mid” (phospho-serine 7) and “late” (phospho-serine 2) CTD marks. We identify gene-class specific patterns and find widespread co-occurrence of the CTD marks. Contrary to its role in 3’ processing of non-coding RNA, the Ser7-P marks are placed early and retained until transcription termination at all Pol II-dependent genes. Chemical-genomic analysis reveals that the promoter-distal Ser7-P marks are not remnants of early phosphorylation, but are placed anew by the CTD kinase Bur1. Consistent with the ability of Bur1 to facilitate transcription elongation and suppress cryptic transcription, high levels of Ser7-P are observed at highly transcribed genes. We propose that Ser7-P could facilitate elongation and suppress cryptic transcription.

Co-occurrence of musculoskeletal pain among female kitchen workers

The co-occurrence of musculoskeletal pain symptoms in seven body sites and their combinations among women in kitchen work were studied. Data on musculoskeletal pain during the past 3 months in the neck, shoulders, forearms/hands, low back, hips, knees and ankles/feet were gathered by questionnaire from 495 female workers (mean age 45 years) in connection with an ergonomic intervention study in municipal kitchens of four cities in Finland. Altogether 122 kitchens (60% of those eligible) participated in the study. The response rate in the participating kitchens was 98%. The 3-month prevalence of any musculoskeletal pain was 87%, the most common sites being the neck (71%), low back (50%) and forearms/hands (49%). About 73% of the subjects had pain in at least two, 36% in four or more, and 10% in 6-7 sites. In pair wise comparisons, e.g. neck pain was associated with pain in other sites with prevalence ratios (PR) varying from 1.3 to 1.6, and ankle or foot pain with ratios between 1.9 and 2.4. The seven pain symptoms occurred in more than 80 different combinations. When the co-occurrence of pain was studied in three larger anatomical areas, i.e. any pain in the axial (neck and low back), upper limb and lower limb areas, subjects reporting concurrent pain in all three were the largest category (36% of the respondents). Altogether 53% of the workers reported pain in at least the axial and upper limb areas, and 48% in at least the axial and lower limb areas. Widespread co-occurrence of musculoskeletal pain symptoms was common among female kitchen workers with slight predominance in the upper body.

Biogeography of Ordovician sponges

Sponges have an unrealized potential importance in biogeographic analysis. Biogeographic patterns determined from our analysis of all published data on distribution of Ordovician genera indicate Early Ordovician sponge faunas have relatively low diversity and are completely dominated by demosponges. Early Ordovician (Ibexian) faunas are characterized by the widespread co-occurrence ofArchaeoscyphiaand the problematicCalathium.This association is commonly found in biohermal structures. Middle Ordovician faunas show an increase in diversity, and two broad associations are differentiated: Appalachian faunas (including Southern China and the Argentine Precordillera) and Great Basin faunas.Late Ordovician faunas show important changes in diversity and provincialism. Hexactinellid and calcareous sponges became important and new demosponge families appeared. Four Mohawkian-Cincinnatian associations are recognized here, including: 1) Midcontinent faunas; 2) Baltic faunas; 3) New South Wales faunas; and 4) Western North American (California and Alaska) faunas. However, two separate biogeographic associations are differentiated based on faunal differences. These are a Pacific association (western North American and New South Wales) and an Atlantic association (Midcontinent Laurentia and Baltica).Distribution of sponge genera and migration patterns are utilized to consider paleogeographic dispositions of the different continental plates, climatic features, and oceanic currents. Such an analysis points to close paleogeographic affinities between the Argentine Precordillera and Laurentian Appalachian faunas. However, significant endemicity and the occurrence of extra-Laurentian genera suggest a relative isolation of the Precordillera terrane during the Late Ibexian-Whiterockian. The study also shows a faunal migration from the Appalachian region to South China during the Middle Ordovician and the migration of faunas from Baltica to Laurentia in the Late Ordovician. The occurrence of Laurentian migrants in New South Wales during the Late Ordovician could be related to inferred oceanic current circulation between these two areas, although other paleogeographic features may be involved.