Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau

Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

BACKGROUND

Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.

RESULTS

We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.

Low-Power, Multi-Transduction Nanosensor Array for Accurate Sensing of Flammable and Toxic Gases

Toxic and flammable gases pose a major safety risk in industrial settings; thus, their portable sensing is desired, which requires sensors with fast response, low-power consumption, and accurate detection. Herein, a low-power, multi-transduction array is presented for the accurate sensing of flammable and toxic gases. Specifically, four different sensors are integrated on a micro-electro-mechanical-systems platform consisting of bridge-type microheaters. To produce distinct fingerprints for enhanced selectivity, the four sensors operate based on two different transduction mechanisms: chemiresistive and calorimetric sensing. Local, in situ synthesis routes are used to integrate nanostructured materials (ZnO, CuO, and Pt Black) for the sensors on the microheaters. The transient responses of the four sensors are fed to a convolutional neural network for real-time classification and regression of five different gases (H₂ , NO₂ , C₂ H₆ O, CO, and NH₃ ). An overall classification accuracy of 97.95%, an average regression error of 14%, and a power consumption of 7 mW per device are obtained. The combination of a versatile low-power platform, local integration of nanomaterials, different transduction mechanisms, and a real-time machine learning strategy presented herein helps advance the constant need to simultaneously achieve fast, low-power, and selective gas sensing of flammable and toxic gases.

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

The arid and semiarid areas experienced remarkable lake shrinkage during recent decades due to intensive human activities and climate change, which would result in unprecedented changes of microeukaryotic communities. However, little is known about how climate change affects the structure and ecological mechanisms of microeukaryotic communities in this area. Here, we used an 18S rRNA gene-based high-throughput sequencing approach to explore the structure, interspecies interaction, and assembly processes of the microeukaryotic community in lake ecosystems of the Inner Mongolia Plateau. As a direct result of climate change, salinity has become the key determinant of the lacustrine microeukaryotic community in this region. The microeukaryotic community in this ecosystem can be divided into three groups: salt (Lake Daihai), brackish (Lake Dalinuoer) and freshwater lakes. Co-occurrence network analysis revealed that salinity shapes the interspecies interactions of the microeukaryotic community. This causes interspecies interactions to change from antagonistic to cooperative with an increase in salinity. Phylogenetic-based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated the microeukaryotic community assembly in lake ecosystems of the Inner Mongolia Plateau, and salinity stress drove the assembly processes of the microeukaryotic community from stochastic to deterministic. Overall, these findings expand the current understanding of interspecies interactions and assembly processes of microeukaryotic communities during climate change in lake ecosystems of the Inner Mongolia Plateau.

Fabrication and characterization of octenyl succinic anhydride modified pullulan micelles for encapsulating curcumin

BACKGROUND

Curcumin has become increasingly popular in functional foods and beverages field as a result of its high biological activity. Nevertheless, the application of curcumin is usually limited by its poor water solubility, low absorption, rapid metabolism and instability. Accordingly, the development of an appropriate wall material is crucial for its effective use. In the present study, curcumin-octenyl succinic anhydride modified pullulan (Cur-OSAP) micelles were successfully prepared by an anti-solvent co-precipitation method.

RESULTS

Octenyl succinic anhydride modified pullulan (OSAP) micelles exhibited the highest encapsulation efficiency (57.31%) and loading capacity (5.73%) of curcumin when the mass ratio of OSAP to curcumin was 10:1 and the degree of substitution of OSAP was 0.0469, at which point Cur-OSAP micelles formed via hydrogen binding and hydrophobic interactions, as confirmed by Fourier transform infrared and fluorescence techniques. The transmission electron microscopy results showed that the Cur-OSAP micelles were roughly spherical in shape with diameters in the approximate range 30-60 nm.

CONCLUSION

The encapsulation of OSAP greatly improved photostability and sustained release properties of curcumin in Cur-OSAP micelles. These findings suggest that OSAP can be used as a carrier to encapsulate and protect hydrophobic food ingredients. © 2021 Society of Chemical Industry.

Chronological and biological aging of the human left ventricular myocardium: Analysis of microRNAs contribution

Aging is the main risk factor for cardiovascular diseases. In humans, cardiac aging remains poorly characterized. Most studies are based on chronological age (CA) and disregard biological age (BA), the actual physiological age (result of the aging rate on the organ structure and function), thus yielding potentially imperfect outcomes. Deciphering the molecular basis of ventricular aging, especially by BA, could lead to major progresses in cardiac research. We aim to describe the transcriptome dynamics of the aging left ventricle (LV) in humans according to both CA and BA and characterize the contribution of microRNAs, key transcriptional regulators. BA is measured using two CA-associated transcriptional markers: CDKN2A expression, a cell senescence marker, and apparent age (AppAge), a highly complex transcriptional index. Bioinformatics analysis of 132 LV samples shows that CDKN2A expression and AppAge represent transcriptomic changes better than CA. Both BA markers are biologically validated in relation to an aging phenotype associated with heart dysfunction, the amount of cardiac fibrosis. BA-based analyses uncover depleted cardiac-specific processes, among other relevant functions, that are undetected by CA. Twenty BA-related microRNAs are identified, and two of them highly heart-enriched that are present in plasma. We describe a microRNA-gene regulatory network related to cardiac processes that are partially validated in vitro and in LV samples from living donors. We prove the higher sensitivity of BA over CA to explain transcriptomic changes in the aging myocardium and report novel molecular insights into human LV biological aging. Our results can find application in future therapeutic and biomarker research.

Habitat heterogeneity, temperature, and primary productivity drive elevational gradients in avian species diversity

AIM

Anticipating and mitigating the impacts of climate change on species diversity in montane ecosystems requires a mechanistic understanding of drivers of current patterns of diversity. We documented the shape of elevational gradients in avian species richness in North America and tested a suite of a priori predictions for each of five mechanistic hypotheses to explain those patterns.

LOCATION

United States.

METHODS

We used predicted occupancy maps generated from species distribution models for each of 646 breeding birds to document elevational patterns in avian species richness across the six largest U.S. mountain ranges. We used spatially explicit biotic and abiotic data to test five mechanistic hypotheses proposed to explain geographic variation in species richness.

RESULTS

Elevational gradients in avian species richness followed a consistent pattern of low elevation plateau-mid-elevation peak (as per McCain, 2009). We found support for three of the five hypotheses to explain the underlying cause of this pattern: the habitat heterogeneity, temperature, and primary productivity hypotheses.

MAIN CONCLUSIONS

Species richness typically decreases with elevation, but the primary cause and precise shape of the relationship remain topics of debate. We used a novel approach to study the richness-elevation relationship and our results are unique in that they show a consistent relationship between species richness and elevation among 6 mountain ranges, and universal support for three hypotheses proposed to explain the underlying cause of the observed relationship. Taken together, these results suggest that elevational variation in food availability may be the ecological process that best explains elevational gradients in avian species richness in North America. Although much attention has focused on the role of abiotic factors, particularly temperature, in limiting species' ranges, our results offer compelling evidence that other processes also influence (and may better explain) elevational gradients in species richness.

Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments

There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35-25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.

Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea

The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.

Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination

Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

Habitat heterogeneity captured by 30-m resolution satellite image texture predicts bird richness across the United States

Species loss is occurring globally at unprecedented rates, and effective conservation planning requires an understanding of landscape characteristics that determine biodiversity patterns. Habitat heterogeneity is an important determinant of species diversity, but is difficult to measure across large areas using field-based methods that are costly and logistically challenging. Satellite image texture analysis offers a cost-effective alternative for quantifying habitat heterogeneity across broad spatial scales. We tested the ability of texture measures derived from 30-m resolution Enhanced Vegetation Index (EVI) data to capture habitat heterogeneity and predict bird species richness across the conterminous United States. We used Landsat 8 satellite imagery from 2013-2017 to derive a suite of texture measures characterizing vegetation heterogeneity. Individual texture measures explained up to 21% of the variance in bird richness patterns in North American Breeding Bird Survey (BBS) data during the same time period. Texture measures were positively related to total breeding bird richness, but this relationship varied among forest, grassland, and shrubland habitat specialists. Multiple texture measures combined with mean EVI explained up to 41% of the variance in total bird richness, and models including EVI-based texture measures explained up to 10% more variance than those that included only EVI. Models that also incorporated topographic and land cover metrics further improved predictive performance, explaining up to 51% of the variance in total bird richness. A texture measure contributed predictive power and characterized landscape features that EVI and forest cover alone could not, even though the latter two were overall more important variables. Our results highlight the potential of texture measures for mapping habitat heterogeneity and species richness patterns across broad spatial extents, especially when used in conjunction with vegetation indices or land cover data. By generating 30-m resolution texture maps and modeling bird richness at a near-continental scale, we expand on previous applications of image texture measures for modeling biodiversity that were either limited in spatial extent or based on coarse-resolution imagery. Incorporating texture measures into broad-scale biodiversity models may advance our understanding of mechanisms underlying species richness patterns and improve predictions of species responses to rapid global change.

A novel homozygous variant in MICOS13/QIL1 causes hepato-encephalopathy with mitochondrial DNA depletion syndrome

BACKGROUND

Mitochondrial DNA depletion syndrome (MTDPS) is part of a group of mitochondrial diseases characterized by a reduction in mitochondrial DNA copy number. Most MTDPS is caused by mutations in genes that disrupt deoxyribonucleotide metabolism.

METHODS

We performed the whole-exome sequencing of a hepato-encephalopathy patient with MTDPS and functional analyses to determine the clinical significance of the identified variant.

RESULTS

Here, whole-exome sequencing of a patient presenting with hepato-encephalopathy and MTDPS identified a novel homozygous frameshift variant, c.13_29del (p.Trp6Profs*71) in MICOS13. MICOS13 (also known as QIL1, MIC13, or C19orf70) is a component of the MICOS complex, which plays crucial roles in the maintenance of cristae junctions at the mitochondrial inner membrane. We found loss of MICOS13 protein and fewer cristae structures in the mitochondria of fibroblasts derived from the patient. Stable expression of a wild-type MICOS13 cDNA in the patients fibroblasts using a lentivirus system rescued mitochondrial respiratory chain complex deficiencies.

CONCLUSION

Our findings suggest that the novel c.13_29del (p.Trp6Profs*71) MICOS13 variant causes hepato-encephalopathy with MTDPS. We propose that MICOS13 is classified as the cause of MTDPS.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Heterogeneity-diversity relationships in sessile organisms: a unified framework

The hypothesis that environmental heterogeneity promotes species richness by increasing opportunities for niche partitioning is a fundamental paradigm in ecology. However, recent studies suggest that heterogeneity-diversity relationships (HDR) are more complex than expected from this niche-based perspective, and often show a decrease in richness at high levels of heterogeneity. These findings have motivated ecologists to propose new mechanisms that may explain such deviations. Here we provide an overview of currently recognised mechanisms affecting the shape of HDRs and present a conceptual model that integrates all previously proposed mechanisms within a unified framework. We also translate the proposed framework into an explicit community dynamic model and use the model as a tool for generating testable predictions concerning how landscape properties interact with species traits in determining the shape of HDRs. Our main finding is that, despite the enormous complexity of such interactions, the predicted HDRs are rather simple, ranging from positive to unimodal patterns in a highly consistent and predictable manner.

National Cancer Institute Alliance for nanotechnology in cancer-Catalyzing research and translation toward novel cancer diagnostics and therapeutics

Nanotechnology has been a burgeoning research field, which is finding compelling applications in several practical areas of everyday life. It has provided novel, paradigm shifting solutions to medical problems and particularly to cancer. In order to accelerate integration of nanotechnology into cancer research and oncology, the National Cancer Institute (NCI) of the National Institutes of Health (NIH) established the NCI Alliance for Nanotechnology in Cancer program in 2005. This effort brought together scientists representing physical sciences, chemistry, and engineering working at the nanoscale with biologists and clinicians working on cancer to form a uniquely multidisciplinary cancer nanotechnology research community. The last 14 years of the program have produced a remarkable body of scientific discovery and demonstrated its utility to the development of practical cancer interventions. This paper takes stock of how the Alliance program influenced melding of disparate research disciplines into the field of nanomedicine and cancer nanotechnology, has been highly productive in the scientific arena, and produced a mechanism of seamless transfer of novel technologies developed in academia to the clinical and commercial space. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Regulatory and Policy Issues in Nanomedicine Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Diagnostic Tools > in vivo Nanodiagnostics and Imaging.

Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle

The number of marine protected areas (MPAs) has increased dramatically in the last decade and poses a major logistic challenge for conservation practitioners in terms of spatial extent and the multiplicity of habitats and biotopes that now require assessment. Photographic assessment by autonomous underwater vehicle (AUV) enables the consistent description of multiple habitats, in our case including mosaics of rock and sediment. As a case study, we used this method to survey the Greater Haig Fras marine conservation zone (Celtic Sea, northeast Atlantic). We distinguished 7 biotopes, detected statistically significant variations in standing stocks, species density, species diversity, and faunal composition, and identified significant indicator species for each habitat. Our results demonstrate that AUV-based photography can produce robust data for ecological research and practical marine conservation. Standardizing to a minimum number of individuals per sampling unit, rather than to a fixed seafloor area, may be a valuable means of defining an ecologically appropriate sampling unit. Although composite sampling represents a change in standard practice, other users should consider the potential benefits of this approach in conservation studies. It is broadly applicable in the marine environment and has been successfully implemented in deep-sea conservation and environmental impact studies. Without a cost-effective method, applicable across habitats, it will be difficult to further a coherent classification of biotopes or to routinely assess their conservation status in the rapidly expanding global extent of MPAs.

Association between human papillomavirus infection and prostate cancer: A global systematic review and meta-analysis

Although an increasing number of studies have been conducted to evaluate the association between human papillomavirus (HPV) infections and distribution of HPV types worldwide with the risk of prostate cancer (PC), the results remain inadequate. Hence, we investigated the association between HPV infection and PC risk using a meta-analysis. Relevant studies from January 1990 to December 2016 were searched in PubMed, Web of sciences, and Scopus databases. Pooled odds ratio (OR) and their corresponding 95% confidence interval (CI) were calculated to find the association between the prevalence of HPV and prostate cancer risk. To do so, data from 24 studies with 5546 prostate cancer cases were pooled in order to evaluate the heterogeneity of chief parameters including study region, specimen type, HPV DNA source, detection technique, publication calendar period, and Gleason score. All statistical analyses were performed using STATA 11 and MedCalc 13. A significant positive association was found between HPV infection and PC risk (OR = 1.281; P = 0.026). The genotype 16 was more frequently found in patients with PC which significantly increased the cancer risk (OR = 1.60; P < 0.001). Age 65 and older could significantly escalate PC risk (OR = 3.564; P < 0.001). Our results clearly favor the potential pathogenetic link between HPV infection and increased risk of PC affirming that HPV infections could play a part in the risk of PC.

Ancient plant DNA in lake sediments

Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America

Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.