Search

Abstract: A 76-year-old female patient presented with a peculiar new exophytic-appearing, flesh-colored skin lesion on her left hallux. Owing to its atypical appearance, the neoplasm was biopsied. Histologic sections demonstrated numerous thickened, anastomosing cord-like structures composed of bland appearing adnexal keratinocytes attached to the epidermis and extending into the superficial dermis. Nearby areas exhibited papillomatosis, epidermal acanthosis, dense hyperparakeratosis, hypergranulosis, and superficial koilocytes, findings consistent with a verruca plantaris. A p16 stain was positive in many of the superficial epidermal keratinocytes. Human papillomavirus typing by in situ hybridization for the most common low-risk and high-risk types was also performed and was negative for these. We herein present an unusual case of a skin lesion which combines features of a poroma with a verruca plantaris. We further review what is known of the relationship between human papillomavirus and poroid neoplasms., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Liver resection for colorectal metastases is affected by a non-negligible recurrence rate. The earlier the recurrence, the worse the prognosis. We analyzed an unexplored topic, i.e., the incidence, predictive factors, and prognostic impact of very early recurrence (≤ 3 months after hepatectomy)., Methods: All consecutive liver resections for colorectal metastases performed between 2004 and 2017 were retrospectively reviewed. Inclusion criteria were available recurrence status at 3 months after resection and follow-up ≥ 12 months., Results: Overall, 484 patients were analyzed; 56 (11.6%) had very early recurrence. Independent predictors were number of metastases (very early recurrence in 3.7% of patients with solitary metastasis, 8.1% of those with 2-9 metastases; 20.0% of those with 10-14 metastases; 44.4% of those with ≥ 15 metastases, p < 0.001) and extrahepatic disease (very early recurrence in 23.2% of patients with vs. 10.1% of those without extrahepatic disease, p = 0.017). Very early recurrence rate in patients with ≥ 15 metastases and simultaneous extrahepatic disease was 71.4%. Patients with very early recurrence had poor survival (5-year survival 17.3% vs. 44.5% of non-very early recurrence patients, p < 0.001), worse than patients with 3-to-6 months recurrence (p = 0.070), and no different from unresected patients (p = 0.114). Fifteen patients with very early recurrence (26.8%) underwent repeated treatment with adequate survival (at 3 years 42.2%), but seven had a further recurrence within 3 months., Conclusions: Very early recurrence occurs in about 12% of patients undergoing aggressive surgery for colorectal metastases. The risk is increased in patients with numerous metastases or extrahepatic disease. Very early recurrence is associated with very poor prognosis, similar to that of unresected patients, and a low chance of effective repeated treatment., (© 2021. The Society for Surgery of the Alimentary Tract.)

Head and neck squamous cell carcinoma (HNSCC) is a molecularly heterogeneous disease, with a 5-year survival rate that still hovers at ~60% despite recent advancements. The advanced stage upon diagnosis, limited success with effective targeted therapy and lack of reliable biomarkers are among the key factors underlying the marginally improved survival rates over the decades. Prevention, early detection and biomarker-driven treatment adaptation are crucial for timely interventions and improved clinical outcomes. Liquid biopsy, analysis of tumour-specific biomarkers circulating in bodily fluids, is a rapidly evolving field that may play a striking role in optimising patient care. In recent years, significant progress has been made towards advancing liquid biopsies for non-invasive early cancer detection, prognosis, treatment adaptation, monitoring of residual disease and surveillance of recurrence. While these emerging technologies have immense potential to improve patient survival, numerous methodological and biological limitations must be overcome before their implementation into clinical practice. This review outlines the current state of knowledge on various types of liquid biopsies in HNSCC, and their potential applications for diagnosis, prognosis, grading treatment response and post-treatment surveillance. It also discusses challenges associated with the clinical applicability of liquid biopsies and prospects of the optimised approaches in the management of HNSCC., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Primary gypsum deposits, which accumulated in the Mediterranean Basin during the so-called Messinian salinity crisis (5.97-5.33 Ma), represent an excellent archive of microbial life. We investigated the molecular fossil inventory and the corresponding compound-specific δ 13 C values of bottom-grown gypsum formed during the first stage of the crisis in four marginal basins across the Mediterranean (Nijar, Spain; Vena del Gesso, Italy; Heraklion, Crete; and Psematismenos, Cyprus). All studied gypsum samples contain intricate networks of filamentous microfossils, whose phylogenetic affiliation has been debated for a long time. Petrographic analysis, molecular fossil inventories (hydrocarbons, alcohols, and carboxylic acids), and carbon stable isotope patterns suggest that the mazes of filamentous fossils represent benthic microbial assemblages dominated by chemotrophic sulfide-oxidizing bacteria; in some of the samples, the body fossils are accompanied by lipids produced by sulfate-reducing bacteria. Abundant isoprenoid alcohols including diphytanyl glycerol diethers (DGDs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), typified by highly variable carbon stable isotope composition with δ 13 C values spanning from -40 to -14‰, reveal the presence of planktic and benthic archaeal communities dwelling in Messinian paleoenvironments. The compound inventory of archaeal lipids indicates the existence of a stratified water column, with a normal marine to diluted upper water column and more saline deeper waters. This study documents the lipid biomarker inventory of microbial life preserved in ancient gypsum deposits, helping to reconstruct the widely debated conditions under which Messinian gypsum formed., (© 2021 The Authors. Geobiology published by John Wiley & Sons Ltd.)

In marine sediments, microorganisms are known to play important roles in nitrogen cycling; however, the composition and quantity of microbes taking part in each process of nitrogen cycling are currently unclear. In this study, two different types of marine sediment samples (shallow bay and deep-sea sediments) in the South China Sea (SCS) were selected to investigate the microbial community involved in nitrogen cycling. The abundance and composition of prokaryotes and seven key functional genes involved in five processes of the nitrogen cycle [nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox)] were presented. The results showed that a higher abundance of denitrifiers was detected in shallow bay sediments, while a higher abundance of microbes involved in ammonia oxidation, anammox, and DNRA was found in the deep-sea sediments. Moreover, phylogenetic differentiation of bacterial amoA, nirS, nosZ, and nrfA sequences between the two types of sediments was also presented, suggesting environmental selection of microbes with the same geochemical functions but varying physiological properties. [ABSTRACT FROM AUTHOR]

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle. [ABSTRACT FROM AUTHOR]

Digital polymerase chain reaction (digital PCR, dPCR) is a direct nucleic acid quantification method, thus requiring no standard curves unlike quantitative real-time PCR (qPCR). Nevertheless, evaluation of the linear dynamic range, accuracy, and precision of an assay or platform is recommended, as there are several potential causes of important non-linearity, bias, and imprecision. Ignoring these quality issues may lead to erroneous quantification. This necessitates an approach akin to the construction of standard curves. We study the pitfalls associated with the evaluation of such an experiment, and provide guidelines for the assessment of linearity, accuracy, and precision in dPCR experiments. We present simulation results and a case study supporting the importance of a thorough evaluation. Further, typically presented plots and statistics may not reveal problems with linearity, accuracy, or precision. We find that a robust weighted least-squares approach is highly advisable, yet may also suffer from an inflated false-positive rate. The proposed assessments are also applicable to other analyses, such as the comparison of results obtained from qPCR and dPCR. A web tool for quality evaluation, dPCalibRate, is available. [ABSTRACT FROM AUTHOR]

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth's biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and "omics" studies in this field. [ABSTRACT FROM AUTHOR]

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bioavailable nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. [ABSTRACT FROM AUTHOR]

Contact chemosensation, or tasting, is a complex process governed by nonvolatile phytochemicals that tell host-seeking insects whether they should accept or reject a plant. During this process, insect gustatory receptors (GRs) contribute to deciphering a host plant's metabolic code. GRs recognise many different classes of nonvolatile compounds; some GRs are likely to be narrowly tuned and others, broadly tuned. Although primary and/or secondary plant metabolites influence the insect's feeding choice, their decoding by GRs is challenging, because metabolites in planta occur in complex mixtures that have additive or inhibitory effects; in diverse forms composed of structurally unrelated molecules; and at different concentrations depending on the plant species, its tissue and developmental stage. Future studies of the mechanism of insect herbivore GRs will benefit from functional characterisation taking into account the spatio-temporal dynamics and diversity of the plant's metabolome. Metabolic information, in turn, will help to elucidate the impact of single ligands and complex natural mixtures on the insect's feeding choice. [ABSTRACT FROM AUTHOR]

Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta-omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community-based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions. [ABSTRACT FROM AUTHOR]

Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns-AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra-unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT-based paleoclimatology and bring about the potential use of uns-AELs as biomarkers for planktonic Euryarchaeota. [ABSTRACT FROM AUTHOR]

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments. [ABSTRACT FROM AUTHOR]

In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles. In contrast to symbiotic species, the heterotrophic fauna exhibited high trophic flexibility among assemblages, suggesting weak trophic links to the metabolic diversity of chemosynthetic primary producers. At both ecosystems, food webs did not appear to be organised through predator-prey links but rather through weak trophic relationships among co-occurring species. Examples of trophic or spatial niche differentiation highlighted the importance of species-sorting processes within chemosynthetic ecosystems. Variability in food web structure, addressed through Bayesian metrics, revealed consistent trends across ecosystems. Food-web complexity significantly decreased with increasing methane concentrations, a common proxy for the intensity of seep and vent fluid fluxes. Although high fluid-fluxes have the potential to enhance primary productivity, they generate environmental constraints that may limit microbial diversity, colonisation of consumers and the structuring role of competitive interactions, leading to an overall reduction of food-web complexity and an increase in trophic redundancy. Heterogeneity provided by foundation species was identified as an additional structuring factor. According to their biological activities, foundation species may have the potential to partly release the competitive pressure within communities of low fluid-flux habitats. Finally, ecosystem functioning in vents and seeps was highly similar despite environmental differences (e.g. physico-chemistry, dominant basal sources) suggesting that ecological niches are not specifically linked to the nature of fluids. This comparison of seep and vent functioning in the Guaymas basin thus provides further supports to the hypothesis of continuity among deep-sea chemosynthetic ecosystems. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is a microbial process in which NH4+ is oxidized to N2 gas with NO2− as an electron acceptor. The anammox process is mediated by bacterial members affiliated with the phylum P lanctomycetes, which are ubiquitously detected from anoxic natural and man-made ecosystems and a key player in the global nitrogen cycle. In the past two decades, phylogenetically different anammox bacteria have been recognized in natural and synthetic ecosystems (i.e. ' C andidatus Kuenenia', ' C andidatus Brocadia', ' C andidatus Jettenia', ' C andidatus Anammoxoglobus' and ' C andidatus Scalindua' genera), and the geographic distributions of these anammox bacteria indicate that they have genus-specific or species-specific habitats. Recently, we revealed the physiological characteristics of ' C a. Jettenia' in addition to ' C a. Kuenenia', ' C a. Brocadia' and ' C a. Scalindua', and, as a result, it is possible to compare the physiological characteristics of the anammox bacteria and discuss their niche partitioning. Therefore, we summarize the current knowledge of anammox bacterial ecology and physiology in this review to assess the potential ecological niche partitioning of anammox bacteria in natural and synthetic ecosystems. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is a relatively new pathway within the N cycle discovered in the late 1990s. This eminent discovery not only modified the classical theory of biological metabolism and matter cycling, but also profoundly influenced our understanding of the energy sources for life. A new member of chemolithoautotrophic microorganisms capable of carbon fixation was found in the vast deep dark ocean. If the discovery of the chemosynthetic ecosystems in the deep-sea hydrothermal vent environments once challenged the old dogma 'all living things depend on the sun for growth,' the discovery of anammox bacteria that are widespread in anoxic environments fortifies the victory over this dogma. Anammox bacteria catalyze the oxidization of NH by using NO as the terminal electron acceptor to produce N. Similar to the denitrifying microorganisms, anammox bacteria play a biogeochemical role of inorganic N removal from the environment. However, unlike heterotrophic denitrifying bacteria, anammox bacteria are chemolithoautotrophs that can generate transmembrane proton motive force, synthesize ATP molecules and further carry out CO fixation through metabolic energy harvested from the anammox process. Although anammox bacteria and the subsequently found ammonia-oxidizing archaea (AOA), another very important group of N cycling microorganisms are both chemolithoautotrophs, AOA use ammonia rather than ammonium as the electron donor and O as the terminal electron acceptor in their energy metabolism. Therefore, the ecological process of AOA mainly takes place in oxic seawater and sediments, while anammox bacteria are widely distributed in anoxic water and sediments, and even in some typical extreme marine environments such as the deep-sea hydrothermal vents and methane seeps. Studies have shown that the anammox process may be responsible for 30%-70% N production in the ocean. In environmental engineering related to nitrogenous wastewater treatment, anammox provides a new technology with low energy consumption, low cost, and high efficiency that can achieve energy saving and emission reduction. However, the discovery of anammox bacteria is actually a hard-won achievement. Early in the 1960s, the possibility of the anammox biogeochemical process was predicted to exist according to some marine geochemical data. Then in the 1970s, the existence of anammox bacteria was further predicted via chemical reaction thermodynamic calculations. However, these microorganisms were not found in subsequent decades. What hindered the discovery of anammox bacteria, an important N cycling microbial group widespread in hypoxic and anoxic environments? What are the factors that finally led to their discovery? What are the inspirations that the analyses of these questions can bring to scientific research? This review article will analyze and elucidate the above questions by presenting the fundamental physiological and ecological characteristics of the marine anammox bacteria and the principles of scientific research. [ABSTRACT FROM AUTHOR]

Biological treatment of wastewaters depends on microbial processes, usually carried out by mixed microbial communities. Environmental and operational factors can affect microorganisms and/or impact microbial community function, and this has repercussion in bioreactor performance. Novel high-throughput molecular methods (metagenomics, metatranscriptomics, metaproteomics, metabolomics) are providing detailed knowledge on the microorganisms governing wastewater treatment systems and on their metabolic capabilities. The genomes of uncultured microbes with key roles in wastewater treatment plants (WWTP), such as the polyphosphate-accumulating microorganism ' Candidatus Accumulibacter phosphatis', the nitrite oxidizer ' Candidatus Nitrospira defluvii' or the anammox bacterium ' Candidatus Kuenenia stuttgartiensis' are now available through metagenomic studies. Metagenomics allows to genetically characterize full-scale WWTP and provides information on the lifestyles and physiology of key microorganisms for wastewater treatment. Integrating metagenomic data of microorganisms with metatranscriptomic, metaproteomic and metabolomic information provides a better understanding of the microbial responses to perturbations or environmental variations. Data integration may allow the creation of predictive behavior models of wastewater ecosystems, which could help in an improved exploitation of microbial processes. This review discusses the impact of meta-omic approaches on the understanding of wastewater treatment processes, and the implications of these methods for the optimization and design of wastewater treatment bioreactors. [ABSTRACT FROM AUTHOR]

Fixed nitrogen is released by anaerobic ammonium oxidation (anammox) and/or denitrification from (marine) ecosystems. Nitrite, the terminal electron acceptor of the anammox process, occurs in nature at very low concentrations and is produced via (micro)aerobic oxidation of ammonium or nitrate reduction. The coupling of sulfide-dependent denitrification to anammox is particularly interesting because besides hydrogen, sulfide is the most important reductant at the chemocline of anoxic marine basins and is abundant within sediments. Although at μ M concentrations, sulfide may be toxic and inhibiting anammox activity, a denitrifying microorganism could convert sulfide and nitrate at sufficiently high rates to allow anammox bacteria to stay active despite an influx of sulfide. To test this hypothesis, a laboratory scale model system containing a co-culture of anammox bacteria and the autotrophic denitrifier S ulfurimonas denitrificans DSM1251 was started. Complementary techniques revealed that the gammaproteobacterial S edimenticola sp. took over the intended role of S u. denitrificans. A stable coculture of anammox bacteria and S edimenticola sp. consumed sulfide, nitrate, ammonium and CO2. Anammox bacteria contributed 65-75% to the nitrogen loss from the reactor. The cooperation between anammox and sulfide-dependent denitrification may play a significant role in environments where sulfur cycling is active and where actual sulfide concentrations stay below μ M range. [ABSTRACT FROM AUTHOR]

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. [ABSTRACT FROM AUTHOR]

Hydrothermal sediments in the Guaymas Basin are covered by microbial mats that are dominated by nitrate-respiring and sulphide-oxidizing B eggiatoa. The presence of these mats strongly correlates with sulphide- and ammonium-rich fluids venting from the subsurface. Because ammonium and oxygen form opposed gradients at the sediment surface, we hypothesized that nitrification is an active process in these B eggiatoa mats. Using biogeochemical and molecular methods, we measured nitrification and determined the diversity and abundance of nitrifiers. Nitrification rates ranged from 74 to 605 μmol N l−1 mat day−1, which exceeded those previously measured in hydrothermal plumes and other deep-sea habitats. Diversity and abundance analyses of archaeal and bacterial ammonia monooxygenase subunit A genes, archaeal 16 S ribosomal RNA pyrotags and fluorescence in situ hybridization confirmed that ammonia- and nitrite-oxidizing microorganisms were associated with B eggiatoa mats. Intriguingly, we observed cells of bacterial and potential thaumarchaeotal ammonia oxidizers attached to narrow, B eggiatoa-like filaments. Such a close spatial coupling of nitrification and nitrate respiration in mats of large sulphur bacteria is novel and may facilitate mat-internal cycling of nitrogen, thereby reducing loss of bioavailable nitrogen in deep-sea sediments. [ABSTRACT FROM AUTHOR]

Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using 15 N isotope pairing incubation experiments, while 16 S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16 S rRNA gene analysis revealed the presence of ' Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes. [ABSTRACT FROM AUTHOR]

Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials. [ABSTRACT FROM AUTHOR]

Although extensive archeological research works have been conducted in the Serteya region in recent years, the Holocene climate history in the Western Dvina Lakeland in Western Russia is still poorly understood. The Neolithic human occupation of the Serteyka lake–river system responded to climate oscillations, resulting in the development of a pile-dwelling settlement between 5.9 and 4.2 ka cal BP. In this paper, we present the quantitative paleoclimatic reconstructions of the Northgrippian stage (8.2–4.2 ka cal BP) from the Great Serteya Palaeolake Basin. The reconstructions were created based on a multiproxy (Chironomidae, pollen and Cladocera) approach. The mean July air temperature remained at 17–20 °C, which is similar to the present temperature in the Smolensk Upland. The summer temperature revealed only weak oscillations during 5.9 and 4.2 ka cal BP. A more remarkable feature during those events was an increase in continentality, manifested by a lower winter temperature and lower annual precipitation. During the third, intermediate oscillation in 5.0–4.7 ka cal BP, a rise in summer temperature and stronger shifts in continental air masses were recorded. It is still unclear if the above-described climate fluctuations are linked to the North Atlantic Oscillation and can be interpreted as an indication of Bond events because only a few high-resolution paleoclimatic reconstructions from the region have been presented and these reconstructions do not demonstrate explicit oscillations in the period of 5.9 and 4.2 ka cal BP. [ABSTRACT FROM AUTHOR]

The article presents a case study of a 33‑year‑old White male with classic EV had an 8‑month history of an infiltrated and keratotic plaque measuring approximately 1 cm along its longest axis on the upper lip. The article discusses that Histopathological analysis showed a malignant epithelial neoplasm involving the epidermis and dermis consisting of numerous clear cells with nuclear atypia; and areas with ductal differentiation were seen, mainly in the dermal component.

Simple Summary: The standard treatment of patients with hepatic and extrahepatic metastases from colorectal cancer is systemic chemotherapy. We assume that this therapy has the same effectiveness on all disease foci, independent of the involved organ. The effectiveness of chemotherapy is assessed by the pathological response rate: the higher the response rate, the higher the effectiveness of chemotherapy. In the present manuscript, we analyzed patients undergoing resection of hepatic and extrahepatic metastases from colorectal cancer after preoperative chemotherapy. We observed unexpected heterogeneity of the response to chemotherapy of distant metastases from colorectal cancer according to the involved organ. Peritoneal metastases had the highest pathological response rate, which was much higher than the hepatic metastases, while lung and lymph node metastases had extremely poor response rates. Such inhomogeneous effectiveness of systemic treatment in different organs open new perspectives in the treatment of colorectal cancer with distant metastases and oncological research. Background: Systemic therapy is the standard treatment for patients with hepatic and extrahepatic colorectal metastases. It is assumed to have the same effectiveness on all disease foci, independent of the involved organ. The present study aims to compare the response rates of hepatic and extrahepatic metastases to systemic therapy. Methods: All consecutive patients undergoing simultaneous resection of hepatic and extrahepatic metastases from colorectal cancer after oxaliplatin- and/or irinotecan-based preoperative chemotherapy were analyzed. All specimens were reviewed. Pathological response to chemotherapy was classified according to tumor regression grade (TRG). Results: We analyzed 45 patients undergoing resection of 134 hepatic and 72 extrahepatic metastases. Lung and lymph node metastases had lower response rates to chemotherapy than liver metastases (TRG 4–5 95% and 100% vs. 67%, p = 0.008, and p = 0.006). Peritoneal metastases had a higher pathological response rate than liver metastases (TRG 1–3 66% vs. 33%, p < 0.001) and non-hepatic non-peritoneal metastases (3%, p < 0.001). Metastases site was an independent predictor of pathological response to systemic therapy. Conclusions: Response to chemotherapy of distant metastases from colorectal cancer varies in different organs. Systemic treatment is highly effective for peritoneal metastases, more so than liver metastases, while it has a very poor impact on lung and lymph node metastases. [ABSTRACT FROM AUTHOR]

Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. Here, the effect of the electron acceptors anthraquinone-disulfonate (AQDS), a humic acids analog, and Fe3+ on anaerobic methane oxidation were assessed by incubation experiments with anoxic Black Sea water containing ANME-1b. Incubation experiments with 13C-methane and AQDS showed a stimulating effect of AQDS on methane oxidation. Fe3+ enhanced the ANME-1b abundance but did not substantially increase methane oxidation. Sodium molybdate, which was added as an inhibitor of sulfate reduction, surprisingly enhanced methane oxidation, possibly related to the dominant abundance of Sulfurospirillum in those incubations. The presented data suggest the potential involvement of ANME-1b in AQDS-enhanced anaerobic methane oxidation, possibly via electron shuttling to AQDS or via interaction with other members of the microbial community. [ABSTRACT FROM AUTHOR]

Meningitis, encephalitis, and myelitis are various forms of acute central nervous system (CNS) inflammation, which can coexist and lead to serious sequelae. Known aetiologies include infections and immune-mediated processes. Despite advances in clinical microbiology over the past decades, the cause of acute CNS inflammation remains unknown in approximately 50% of cases. High-throughput sequencing was performed to search for viral sequences in cerebrospinal fluid (CSF) samples collected from 26 patients considered to have acute CNS inflammation of unknown origin, and 10 patients with defined causes of CNS diseases. In order to better grasp the clinical significance of viral sequence data obtained in CSF, 30 patients without CNS disease who had a lumbar puncture performed during elective spinal anaesthesia were also analysed. One case of human astrovirus (HAstV)-MLB2-related meningitis and disseminated infection was identified. No other viral sequences that can easily be linked to CNS inflammation were detected. Viral sequences obtained in all patient groups are discussed. While some of them reflect harmless viral infections, others result from reagent or sample contamination, as well as index hopping. Altogether, this study highlights the potential of high-throughput sequencing in identifying previously unknown viral neuropathogens, as well as the interpretation issues related to its application in clinical microbiology. [ABSTRACT FROM AUTHOR]

Byline: Bruno de. Souza, Neusa. Sakai Valente, Stephen. Tyring, Walmar. Pereira de Olveira Sir, Epidermodysplasia verruciformis (EV) is a rare skin disease characterized by abnormalities of cell-mediated immunity, disseminated infection [...]