Pfp-fm: an accelerated FM-index

FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. In 2022, Deng et al. [2] proposed parsing genomic data by induced suffix sorting, and showed that the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing-which takes parameters that let us tune the average length of the phrases-instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38, and is consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it seems our method accelerates the performance of count over all state-of-the-art methods with a moderate increase in the memory. The source code for PFP - FM is available at https://github.com/AaronHong1024/afm .

A ∼5000 year multiproxy record of summer climate in NE Greenland

The High Arctic plays a vital role in Earth's climate system, and its ecosystems are highly sensitive to global climate change. High Arctic lakes are valuable sentinels of climate change, as their sediments integrate long-term natural climatic fluctuations and anthropogenic influences. Here, we present a high-resolution ∼5000 year-reconstruction of NE Greenland climate variability from Aucella Lake (74°N, 20°E) based on physical, chemical, and biological properties of lake sediments. We use CT-scans, hyperspectral imaging, organic matter, XRD, and diatom analyses to show that changing air temperatures were controlled by a mix of regional climatic changes and local landscape feedbacks. The latest Mid-Holocene (∼5.0-3.8 cal. ka BP) was characterized by relatively warmer conditions, while the onset of the Late-Holocene was marked by abrupt temperature decreases that coincided with the beginning of glacial advances elsewhere (∼3.8-3.4 cal. ka BP). From ∼3.4-2.4 cal. ka BP, the sedimentary record indicated progressive warming, with temperature peaking during the Medieval Climate Anomaly, although temperature rises were punctuated by abrupt, short-lived cold periods. From ∼1.1-0.05 cal. ka BP, the influence of landscape factors over the system diminished. Sedimentary indicators suggested a transition towards a colder, more humid climate, coinciding with the beginning of the Little Ice Age, that was characterized by a marked decrease in air temperature that reached minimum values at the end of this period. The last 50 years at Aucella Lake were marked by abrupt temperature rises, consistent with recently observed anthropogenic global warming. Our results illustrate the importance of high-resolution multiproxy studies for accurately characterizing lake linkages to their environment and climate.

PFP-FM: An Accelerated FM-index

FM-indexes are a crucial data structure in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer random accesses than character-based indexes, and thus support faster searches. Since DNA lacks natural word-boundaries, however, it is necessary to parse it somehow before applying word-based FM-indexing. Last year, Deng et al. [2] proposed parsing genomic data by induced suffix sorting, and showed the resulting word-based FM-indexes support faster counting queries than standard FM-indexes when patterns are a few thousand characters or longer. In this paper we show that using prefix-free parsing-which takes parameters that let us tune the average length of the phrases-instead of induced suffix sorting, gives a significant speedup for patterns of only a few hundred characters. We implement our method and demonstrate it is between 3 and 18 times faster than competing methods on queries to GRCh38, and is consistently faster on queries made to 25,000, 50,000 and 100,000 SARS-CoV-2 genomes. Hence, it seems our method accelerates the performance of count over all state-of-the-art methods with a minor increase in the memory. The source code for PFP-FM is available at https://github.com/marco-oliva/afm.

First-in-class Microbial Ecosystem Therapeutic 4 (MET4) in combination with immune checkpoint inhibitors in patients with advanced solid tumors (MET4-IO trial)

BACKGROUND

The intestinal microbiome has been associated with response to immune checkpoint inhibitors (ICIs) in humans and causally implicated in ICI responsiveness in animal models. Two recent human trials demonstrated that fecal microbiota transplant (FMT) from ICI responders can rescue ICI responses in refractory melanoma, but FMT has specific limitations to scaled use.

PATIENTS AND METHODS

We conducted an early-phase clinical trial of a cultivated, orally delivered 30-species microbial consortium (Microbial Ecosystem Therapeutic 4, MET4) designed for co-administration with ICIs as an alternative to FMT and assessed safety, tolerability and ecological responses in patients with advanced solid tumors.

RESULTS

The trial achieved its primary safety and tolerability outcomes. There were no statistically significant differences in the primary ecological outcomes; however, differences in MET4 species relative abundance were evident after randomization that varied by patient and species. Increases in the relative abundance of several MET4 taxa, including Enterococcus and Bifidobacterium, taxa previously associated with ICI responsiveness, were observed and MET4 engraftment was associated with decreases in plasma and stool primary bile acids.

CONCLUSIONS

This trial is the first report of the use of a microbial consortium as an alternative to FMT in advanced cancer patients receiving ICI and the results justify the further development of microbial consortia as a therapeutic co-intervention for ICI treatment in cancer.

A route for the top-down fabrication of ordered ultrathin GaN nanowires

We introduce a facile route for the top-down fabrication of ordered arrays of GaN nanowires with aspect ratios exceeding 10 and diameters below 20 nm. Highly uniform thin GaN nanowires are first obtained by lithographic patterning a bilayer Ni/SiN_xhard mask, followed by a combination of dry and wet etching in KOH. The SiN_xis found to work as an etch stop during wet etching, which eases reproducibility. Arrays with nanowire diameters down to (33 ± 5) nm can be achieved with a uniformity suitable for photonic applications. Next, a scheme for digital etching is demonstrated to further reduce the nanowire diameter down to 5 nm. However, nanowire breaking or bundling is observed for diameters below ≈20 nm, an effect that is associated to capillary forces acting on the nanowires during sample drying in air. Explicit calculations of the nanowire buckling states under capillary forces indicate that nanowire breaking is favored by the incomplete wetting of water on the substrate surface during drying. The observation of intense nanowire photoluminescence at room-temperature indicates good compatibility of the fabrication route with optoelectronic applications. The process can be principally applied to any GaN/SiN_xnanostructures and allows regrowth after removal of the SiN_xmask.

Recursive Prefix-Free Parsing for Building Big BWTs

Prefix-free parsing is useful for a wide variety of purposes including building the BWT, constructing the suffix array, and supporting compressed suffix tree operations. This linear-time algorithm uses a rolling hash to break an input string into substrings, where the resulting set of unique substrings has the property that none of the substrings' suffixes (of more than a certain length) is a proper prefix of any of the other substrings' suffixes. Hence, the name prefix-free parsing. This set of unique substrings is referred to as the dictionary . The parse is the ordered list of dictionary strings that defines the input string. Prior empirical results demonstrated the size of the parse is more burdensome than the size of the dictionary for large, repetitive inputs. Hence, the question arises as to how the size of the parse can scale satisfactorily with the input. Here, we describe our algorithm, recursive prefix-free parsing , which accomplishes this by computing the prefix-free parse of the parse produced by prefix-free parsing an input string. Although conceptually simple, building the BWT from the parse-of-the-parse and the dictionaries is significantly more challenging. We solve and implement this problem. Our experimental results show that recursive prefix-free parsing is extremely effective in reducing the memory needed to build the run-length encoded BWT of the input. Our implementation is open source and available at https://github.com/marco-oliva/r-pfbwt .

Evaluation of Heavy Metals in Vegetables from Two Origins Marketed in Northern Peru

The objective of the study was to evaluate the concentration of arsenic, chromium, cadmium, and lead in onion (Allium fistulosum and Allium cepa), tomato (Solanum lycopersicum), and celery (Apium graveolens) from two origins (local - Chachapoyas province and from the coast-province of Chiclayo) that are sold in the model market of the city of Chachapoyas. Six samples were taken on three different dates in November 2020, which were collected by non-probabilistic sampling (by convenience), which allowed choosing the most appropriate sample (according to its origin). For the determination of heavy metals, the Agilent 4100 MP-AES spectrometer was used. The concentration of As, Cr, and Cd in the vegetables remained below the Maximum Allowable Limits of the international standards with which they were compared; however, the concentration of Pb exceeded the Maximum Allowable Limits in all the samples analyzed, obtaining the lowest value in the celery samples from the local origin (0.15 mg.kg-1) and the highest value in the tomato samples from the coast (0.21 mg.kg-1). Therefore, it is concluded that only Pb is higher than the Maximum Allowable Limits with which it was compared.

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes

BACKGROUND

Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).

RESULTS

Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher ARG recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.

CONCLUSIONS

TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.

Variation in the Alcohol Components of Coffea arabica L. Wastewater Distillate Fermented Under Different Conditions

Coffee is the second-most consumed beverage in the world, and its high demand is covered by countries such as Peru, where the waste generated in production causes environmental pollution. We sought to determine the concentration of alcohol components and other volatiles compounds present in the distillate, after fermenting wastewater from the first wash in the wet processing of Coffea arabica var. catimor under five conditions: C1 (pasteurized + 0.325 g sucrose + 8.000 g S. cerevisiae), C2 = (pasteurized + 8.000 g S. cerevisiae), C3 (0.325 g sucrose + 8.000 g S. cerevisiae), C4 = (8.000 g S. cerevisiae), and C5 = (natural state). The solid-phase microextraction technique was used to determine the composition of the distillates by gas chromatography (GC). 35 components were detected, 11 of them under all conditions. Ethanol was the most abundant element in all five fermentation conditions. Condition 1 shows the highest value at 97.29 μg.mL-1, though all five concentrations can be considered high. This study shows that wastewater from the wet processing of coffee can have agro-industrial use as a value-added product. Postharvest Peruvian coffee is amenable to strategies aligned with the sustainable development goal of reducing food losses along production and supply chains.

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

BACKGROUND

Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.

RESULTS

We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2-0.9). On semi-synthetic metagenomic data-external test-on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.

CONCLUSIONS

AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.

Finding Maximal Exact Matches Using the r-Index

Efficiently finding maximal exact matches (MEMs) between a sequence read and a database of genomes is a key first step in read alignment. But until recently, it was unknown how to build a data structure in [Formula: see text] space that supports efficient MEM finding, where r is the number of runs in the Burrows-Wheeler Transform. In 2021, Rossi et al. showed how to build a small auxiliary data structure called thresholds in addition to the r-index in [Formula: see text] space. This addition enables efficient MEM finding using the r-index. In this article, we present the tool that implements this solution, which we call MONI. Namely, we give a high-level view of the main components of the data structure and show how the source code can be downloaded, compiled, and used to find MEMs between a set of sequence reads and a set of genomes.

MONI: A Pangenomic Index for Finding Maximal Exact Matches

Recently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to build the r-index efficiently via a technique called prefix-free parsing (PFP) and demonstrated its effectiveness for exact pattern matching. Exact pattern matching can be leveraged to support approximate pattern matching, but the r-index itself cannot support efficiently popular and important queries such as finding maximal exact matches (MEMs). To address this shortcoming, Bannai et al. introduced the concept of thresholds, and showed that storing them together with the r-index enables efficient MEM finding-but they did not say how to find those thresholds. We present a novel algorithm that applies PFP to build the r-index and find the thresholds simultaneously and in linear time and space with respect to the size of the prefix-free parse. Our implementation called MONI can rapidly find MEMs between reads and large-sequence collections of highly repetitive sequences. Compared with other read aligners-PuffAligner, Bowtie2, BWA-MEM, and CHIC- MONI used 2-11 times less memory and was 2-32 times faster for index construction. Moreover, MONI was less than one thousandth the size of competing indexes for large collections of human chromosomes. Thus, MONI represents a major advance in our ability to perform MEM finding against very large collections of related references.

Bioassay-based ecotoxicological investigation on marine and freshwater impact of cigarette butt littering

Despite representing an extremely relevant portion (20-40%) of worldwide coastal litter, cigarette butts are still an underestimate environmental issue of limited scientific interest. Public authorities of different countries promote active removal of cigarette butts, but the issue remains problematic in terms of aesthetic, environmental and health-related impacts. There are few studies on the environmental side-effects of smoked cigarette butt litter despite being a worldwide issue. In this work, two ecotoxicological bioassay batteries were adopted to evaluate the environmental consequences of cigarette butt water-soluble ingredient release in both marine water and freshwater. Marine assays were generally more affected compared to freshwater. Interesting outcomes were observed with crustacean tests, showing a lower effect of smoked cigarette butt leachate when tested at maximum concentration. This finding were supported by heartbeat measures of Daphnia magna, which were accelerated at 100% of smoked cigarette butt leachate.

Portable nanopore analytics: are we there yet?

MOTIVATION

Oxford Nanopore technologies (ONT) add miniaturization and real time to high-throughput sequencing. All available software for ONT data analytics run on cloud/clusters or personal computers. Instead, a linchpin to true portability is software that works on mobile devices of internet connections. Smartphones' and tablets' chipset/memory/operating systems differ from desktop computers, but software can be recompiled. We sought to understand how portable current ONT analysis methods are.

RESULTS

Several tools, from base-calling to genome assembly, were ported and benchmarked on an Android smartphone. Out of 23 programs, 11 succeeded. Recompilation failures included lack of standard headers and unsupported instruction sets. Only DSK, BCALM2 and Kraken were able to process files up to 16 GB, with linearly scaling CPU-times. However, peak CPU temperatures were high. In conclusion, the portability scenario is not favorable. Given the fast market growth, attention of developers to ARM chipsets and Android/iOS is warranted, as well as initiatives to implement mobile-specific libraries.

AVAILABILITY AND IMPLEMENTATION

The source code is freely available at: https://github.com/marco-oliva/portable-nanopore-analytics.

Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation

Antimicrobial resistance (AMR) is a significant and growing public health threat. Sequencing of bacterial isolates is becoming more common, and therefore automatic identification of resistant bacterial strains is of pivotal importance for efficient, wide-spread AMR detection. To support this approach, several AMR databases and gene identification algorithms have been recently developed. A key problem in AMR detection, however, is the need for computational approaches detecting potential novel AMR genes or variants, which are not included in the reference databases. Toward this direction, here we study the relation between AMR and relative solvent accessibility (RSA) of protein variants from an in silico perspective. We show how known AMR protein variants tend to correspond to exposed residues, while on the contrary their susceptible counterparts tend to be buried. Based on these findings, we develop RSA-AMR, a novel relative solvent accessibility-based AMR scoring system. This scoring system can be applied to any protein variant to estimate its propensity of altering the relative solvent accessibility, and potentially conferring (or hindering) AMR. We show how RSA-AMR score can be integrated with existing AMR detection algorithms to expand their range of applicability into detecting potential novel AMR variants, and provide a ten-fold increase in Specificity. The two main limitations of RSA-AMR score is that it is designed on single point changes, and a limited number of variants was available for model learning.

Antimicrobial resistance gene shuffling and a three-element mobilisation system in the monophasic Salmonella typhimurium strain ST1030

In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harboured by the Salmonella Typhimurium monophasic variant 1,4,[5],12:i:- strain ST1030. Of the three identified RUs two were chromosomal, RU1 (IS26-bla_TEM-1-IS26-strAB-sul2- IS26) and RU2 (IS26-tetR(B)-tetA(B)-ΔIS26), and one, RU3 (a sul3-associated class 1 integron with cassette array dfrA12-orfF-aadA2-cmlA1-aadA1), was embedded in a Tn21-derived element harboured by the conjugative I1 plasmid pST1030-1A. IS26 elements mediated the antimicrobial resistance gene (ARG) shuffling and this gave rise to pST1030-1A derivatives with different sets of ARGs. ST1030 also harboured two ColE1-like plasmids of which one, pST1030-2A, was mobilisable and the target of an intracellular translocation of the Tn21-derived element; the second (pST1030-3) was an orphan mob-associated oriT plasmid co-transferred with pST1030-1A and pST1030-2A. pST1030-2A and pST1030-3 also carried a parA gene and a type III restriction modification system, respectively. Overall analysis of our data reinforces the role played by IS26, Tn21-derived elements and non-conjugative plasmids in the spread of ARGs and supplies the first evidence, at least in Salmonella, for the identification of a natural isolate harbouring a three-element mobilisation system in the same cell.

Atlantic and Mediterranean populations of the widespread serpulid Ficopomatus enigmaticus: Developmental responses to carbon nanotubes

Ficopomatus enigmaticus was adopted as model species for ecotoxicological bioassay, with its larval development as endpoint. Two different populations of the same species, collected in areas far from each other (Mediterranean Sea and Atlantic Ocean), were exposed to multi-walled carbon nanotubes, a class of emerging pollutants with a constantly increasing relevance in the landscape of nanomaterials production. Moreover, a molecular analysis based on Cyt b amplification and sequencing, was carried out to confirm that both populations belong to the same species. The aim of the present work was to strengthen existing results about F. enigmaticus relevance in ecotoxicological bioassays, adding the variable of population effect. For both populations the concentration-response curve of effect at different toxicant concentrations was similar and, at certain concentrations, overlapping, confirming the ecological relevance of the assay. These results posed an interesting acceptance on the introduction of this species as model in ecotoxicological bioassay scenery, underlining the relevance of a widespread wild species to compare effects of chemicals and environmental samples over large distances using the same bioassay.

Physiological Basis of Salt Stress Tolerance in a Landrace and a Commercial Variety of Sweet Pepper (Capsicum annuum L.)

Salt stress is one of the most impactful abiotic stresses that plants must cope with. Plants’ ability to tolerate salt stress relies on multiple mechanisms, which are associated with biomass and yield reductions. Sweet pepper is a salt-sensitive crop that in Mediterranean regions can be exposed to salt build-up in the root zone due to irrigation. Understanding the physiological mechanisms that plants activate to adapt to soil salinization is essential to develop breeding programs and agricultural practices that counteract this phenomenon and ultimately minimize yield reductions. With this aim, the physiological and productive performances of Quadrato D’Asti, a common commercial sweet pepper cultivar in Italy, and Cazzone Giallo, a landrace of the Campania region (Italy), were compared under different salt stress treatments. Quadrato D’Asti had higher tolerance to salt stress when compared to Cazzone Giallo in terms of yield, which was associated with higher leaf biomass vs. fruit ratio in the former. Ion accumulation and profiling between the two genoptypes revealed that Quadrato D’Asti was more efficient at excluding chloride from green tissues, allowing the maintenance of photosystem functionality under stress. In contrast, Cazzone Giallo seemed to compartmentalize most sodium in the stem. While sodium accumulation in the stems has been shown to protect shoots from sodium toxicity, in pepper and/or in the specific experimental conditions imposed, this strategy was less efficient than chloride exclusion for salt stress tolerance.

Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is currently the most commonly identified antibiotic-resistant pathogen in US hospitals. Resistance to methicillin is carried by SCCmec genetic elements. Multilocus sequence typing (MLST) covers internal fragments of seven housekeeping genes of S. aureus. In conjunction with mec typing, MLST has been used to create an international nomenclature for S. aureus. MLST sequence types with a single nucleotide polymorphism (SNP) considered distinct. In this work, relationships among MLST SNPs and methicillin/oxacillin resistance or susceptibility were studied, using a public data base, by means of cross-tabulation tests, multivariable (phylogenetic) logistic regression (LR), decision trees, rule bases, and random forests (RF). Model performances were assessed through multiple cross-validation. Hierarchical clustering of SNPs was also employed to analyze mutational covariation. The number of instances with a known methicillin (oxacillin) antibiogram result was 1526 (649), where 63% (54%) was resistant to methicillin (oxacillin). In univariable analysis, several MLST SNPs were found strongly associated with antibiotic resistance/susceptibility. A RF model predicted correctly the resistance/susceptibility to methicillin and oxacillin in 75% and 63% of cases (cross-validated). Results were similar for LR. Hierarchical clustering of the aforementioned SNPs yielded a high level of covariation both within the same and different genes; this suggests strong genetic linkage between SNPs of housekeeping genes and antibiotic resistant associated genes. This finding provides a basis for rapid identification of antibiotic resistant S. arues lineages using a small number of genomic markers. The number of sites could subsequently be increased moderately to increase the sensitivity and specificity of genotypic tests for resistance that do not rely on the direct detection of the resistance marker itself.

Effects of copper on larvae of the marbled crab Pachygrapsus marmoratus (Decapoda, Grapsidae): Toxicity test and biochemical marker responses

The importance of trace elements in ecotoxicological investigations is a well-known issue when monitoring polluted areas such as commercial harbors. Copper represents one of the most common metal contaminants, often detected in these areas as it is widely employed in various fields and has many sources of inflow in the marine environment. Pachygrapsus marmoratus is a widespread intertidal crab species that has been extensively studied in ecology, ethology and population genetics. Ecotoxicological studies have also been performed, exclusively on the adult stage. In the present study we investigated the mortality and biochemical (oxidative stress and neurotoxicity) responses of P. marmoratus larvae exposure to environmental relevant concentration of copper. Results showed dose-dependent responses in terms of larval mortality, with a calculated LC₅₀ value of 0.5 mg/L of Cu²⁺. The LC₅₀ concentration was used as the starting point for subsequent biochemical response evaluation. Results also demonstrated dose-dependent activation of antioxidant systems assuming a compensatory antioxidant activity to prevent higher cellular damage when larvae were exposed to the highest concentrations of copper. Moreover, a significant enhancement of neurotransmitter activities was observed, assuming a possible direct interaction of copper with the enzymes or an increase of free copper ion aliquot into the cells.

Ficopomatus enigmaticus larval development assay: An application for toxicity assessment of marine sediments

Ficopomatus enigmaticus is a serpulid polychaete, reef-forming, dioecious gamete spawner throughout different seasons and in different salinity conditions. Due to these characteristics, its candidacy as a model organism to monitor both marine and brackish matrices was assessed. Marine sediments collected in a polluted area near the port of Ancona (Italy) were used as case study. Besides the chemical characterization of sediments, the larval development of F. enigmaticus was adopted as an assay for ecotoxicological assessment of sediments in addition to a regulatory bioassay battery with different organisms and endpoints. The quality of sediments was classified according to the Italian Ministerial Decree for sediment management (Ministerial Decree 173, 2016) by using the SEDI-QUAL-SOFT® (ver. 109.0) software developed by the Italian Environmental Protection Agency (ISPRA). The F. enigmaticus larval development assay showed a quite similar sensitivity to C. gigas larval development assays, indicating its potential use in a regulatory battery of bioassays.

Immune biomarkers of response to immune-checkpoint inhibitors in head and neck squamous cell carcinoma

Anti-programmed cell death protein 1 (PD-1) agents have become the standard of care for platinum-refractory recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) and are currently being evaluated in various disease settings. However, despite the gain in overall survival seen in some of the clinical trials, the majority of patients display primary resistance and do not benefit from these agents. Taking into consideration the potentially severe immune-related toxicities and their high cost, the search for predictive biomarkers of response is crucial. Besides Programmed death ligand-1 (PD-L1) expression, other biomarkers such as immune infiltration, tumor mutational burden or immune-gene expression profiling have been explored, but none of them has been validated in this disease. Among these, the microbiota has recently garnered tremendous interest since it has proven to influence the efficacy of PD-1 blockade in some tumor types. With the accumulating evidence on the effect of the microbiota in HNSCC tumorigenesis and progression, the study of its potential role as a predictive immune biomarker is warranted. This review examines the available evidence on emerging immune predictive biomarkers of response to anti-PD-1/PD-L1 therapy in HNSCC, introducing the microbiota and its potential use as a predictive immune biomarker in this disease.

Late Quaternary environmental dynamics in Lenin Peak area (Pamir Mountains, Kyrgyzstan)

The Pamir Mountains include peaks exceeding 7000 m, such as Lenin Peak (7134 m) in the northern Zaalai Range. Here, we examine the distribution of soils and geomorphological processes and landforms in its northern slope, from the highest glaciated environments until Alai valley floor. We present the first geomorphological map of the study area as well as an accurate description the main geomorphological units in order to reconstruct landscape dynamics in the area from Quaternary cold stages until present-day. Five main units are distributed: (1) valley floor (2900-3040 m), an area that must have been ice-free during Quaternary glaciations and is currently being reshaped by glaciofluvial processes, with a large alluvial fan reworked by aeolian activity; (2) hummocky terrain (3040-3500 m) including two moraine systems left by a piedmont glacier during the Last Glaciation as well as hilly deposits originated by a catastrophic rockfall event; (3) U-shaped glacial valley (3500-3800 m), including some moraine ridges as well as a sedimentary cover composed of glacial till that is being eroded by fluvial and mass-wasting processes; (4) high mountain valleys (up to 4600-4800 m) adjacent to the main valley floor with small cirque and alpine glaciers and widespread periglacial processes in ice-free environments; (5) glaciers flowing from the Lenin Peak summit until the foot of the mountain, where they form a debris-covered (surge-type) glacier. The existence of abundant glacial, periglacial and rockfall deposits (moraines, till, erratic boulders) allows inferring five different environmental stages since the Last Glaciation. The latest glacial advances took place during the 20th century and the Little Ice Age and deposited two moraine systems near the glacial front. The occurrence of active rock glaciers and protalus lobes indicates that the limit of permafrost conditions is now located at 3400-3500 m, with seasonal frozen ground in lower areas.

Physiological, biochemical and molecular responses to water stress and rehydration in Mediterranean adapted tomato landraces

Mediterranean tomato landraces adapted to arid environments represent an option to counteract drought, and to address the complexity of responses to water deficit and recovery, which is a crucial component of plant adaptation mechanisms. We investigated physiological, biochemical and molecular responses of two Mediterranean tomato landraces, 'Locale di Salina' (Lc) and 'Pizzutello di Sciacca' (Pz) under two dehydration periods and intermediate rehydration in greenhouse pot experiments. Relationship between CO₂ assimilation (A) and stomatal conductance under severe water stress (g_s  < 0.05 mol·m^-2 ·s^-1 ) indicated the occurrence of stomatal and non-stomatal limitations of photosynthesis. Gas exchange promptly recovered within 2-3 days of rehydration. ABA and g_s showed a strict exponential relationship. Both leaf ABA and proline peaked under severe water stress. Lc showed higher accumulation of ABA and higher induction of the expression of both NCED and P5CS genes than Pz. Poly(ADP-ribose) polymerase increased during imposition of stress, mainly in Lc, and decreased under severe water stress. The two landraces hardly differed in their physiological performance. Under severe water stress, g_s showed low sensitivity to ABA, which instead controlled stomatal closure under moderate water stress (g_s  > 0.15 mol·m^-2 ·s^-1 ). The prompt recovery after rehydration of both landraces confirmed their drought-tolerant behaviour. Differences between the two landraces were instead observed at biochemical and molecular levels.

Early-drug development in the era of immuno-oncology: are we ready to face the challenges?

The classical development of drugs has progressively faded away, and we are currently in an era of seamless drug-development, where first-in-human trials include unusually big expansion cohorts in the search for early signs of activity and rapid regulatory approval. The fierce competition between different pharmaceutical companies and the hype for immune combinations obliges us to question the current way in which we are evaluating these drugs. In this review, we discuss critical issues and caveats in immunotherapy development. A particular emphasis is put on the limitations of pre-clinical toxicology studies, where both murine models and cynomolgus monkeys have underpredicted toxicity in humans. Moreover, relevant issues surrounding dose determination during phase I trials, such as dose-escalation methods or flat versus body-weight dosing, are discussed. A proposal of how to face these different challenges is offered, in order to achieve maximum efficacy with minimum toxicity for our patients.

Bloodstream infection in patients with head and neck cancer: a major challenge in the cetuximab era

PURPOSE

To assess the impact of bloodstream infection (BSI) in patients with head and neck cancer (HNC) in the cetuximab era.

METHODS

We prospectively analysed the epidemiology, microbiology and outcomes of 51 BSI episodes occurring in 48 patients with HNC (2006-2017). We performed a retrospective matched-cohort study (1:2) to determine the risk factors for BSI. Finally, we compared patients who died with those who survived to identify risk factors for mortality.

RESULTS

The most frequent HNC localization was the oropharynx (43%), and pneumonia was the most frequent source (25%). Gram-positive BSI occurred in 55% cases, mainly due to Streptococcus pneumoniae (21%), and among Gram-negatives, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most frequent. Hypoalbuminemia (OR 8.4; 95% CI, 3.5-19.9), previous chemotherapy (OR, 3.2; 95% CI, 1.3-7.4) and cetuximab therapy (OR, 2.8; 95% CI, 1.6-6.7) were significant risk factors for BSI. Patients with BSI had a higher overall case-fatality rate than patients without BSI (OR, 4.4; 95% CI, 1.7-11.8). Hypoalbuminemia was an independent risk factor for the early (7 day) and overall (30 day) case-fatalities, with ORs of 0.8 (95% CI, 0.6-0.9) and 0.8 (95% CI, 0.7-0.97), respectively. The presence of comorbidities (OR, 7; 95% CI, 1.4-34) was also an independent risk factor for overall case-fatality.

CONCLUSIONS

BSI causes high mortality in patients with HNC and is most often secondary to pneumonia. It occurs mainly among patients with hypoalbuminemia who receive treatment with cetuximab or chemotherapy. The development of BSI in patients with HNC impairs their outcome, especially in the presence of hypoalbuminemia and comorbidities.

Spatial characterization of glacial and periglacial landforms in the highlands of Sierra Nevada (Spain)

Sierra Nevada constitutes the southernmost and highest massif in the Iberian Peninsula, with elevations exceeding 3000m. Two large glacial advances were recorded during the Last Glaciation and several minor advances occurred until the Early Holocene. Since then, periglacial activity has prevailed above 2500m. Here, we present a new and more accurate geomorphological map of the highlands of Sierra Nevada, integrating in a GIS environment i) high resolution satellite imagery, ii) topographic data, and iii) field observations. This approach has allowed a better characterization of the spatial extent of cold-climate morphogenic processes and associated landforms formed during the Last Glaciation and subsequent deglaciation. Despite its extension and high altitude, the steep relief of Sierra Nevada and its southern location conditioned a significantly lower glaciated surface (104.6km²) with respect to other Iberian massifs. We have also inferred the paleoclimatic conditions of the study area through the calculation of Equilibrium Line Altitudes (ELAs). The distribution of the lowest moraines suggests an ELA for the maximum glacial extent at 2525m in the northern slope and 2650m in the southern side, increasing towards the east. Local ELA differences are related to: (i) the influence of the warmer Mediterranean Sea in contrast to the cooler Atlantic Ocean, (ii) the climate with more continental characteristics on the northern slope, and (iii) the microscale control of the local topography. Mean annual air temperatures in the ice-free summit plateaus were between -4/-6°C during the maximum local glacial extent, determining permafrost conditions with intense periglacial dynamics. Rock glaciers and protalus lobes developed until 2500m, the lowest boundary for permafrost regime. The distribution of other glacial and periglacial landforms within the limits of the maximum ice extent provides evidence to better understand the extent of subsequent glacial stages and post-glacial landscape evolution in Sierra Nevada.

Glacial stages and post-glacial environmental evolution in the Upper Garonne valley, Central Pyrenees

The maximum glacial extent in the Central Pyrenees during the Last Glaciation is known to have occurred before the global Last Glacial Maximum, but the succession of cold events afterwards and their impact on the landscape are still relatively unknown. This study focuses on the environmental evolution in the upper valley of the Garonne River since the Last Glaciation. Geomorphological mapping allows analysis of the spatial distribution of inherited and current processes and landforms in the study area. The distribution of glacial records (moraines, till, erratic boulders, glacial thresholds) suggests the existence of four glacial stages, from the maximum expansion to the end of the glaciation. GIS modeling allows quantification of the Equilibrium Line Altitude, extent, thickness and volume of ice in each glacial stage. During the first stage, the Garonne glacier reached 460m in the Loures-Barousse-Barbazan basin, where it formed a piedmont glacier 88km from the head and extended over 960km². At a second stage of glacier stabilization during the deglaciation process, the valley glaciers were 12-23km from the head until elevations of 1000-1850m, covering an area of 157km². Glaciers during stage three remained isolated in the upper parts of the valley, at heights of 2050-2200m and 2.6-4.5km from the head, with a glacial surface of 16km². In stage four, cirque glaciers were formed between 2260m and 2590m, with a length of 0.4-2km and a glacial area of 5.7km². Also, the wide range of periglacial, slope, nival and alluvial landforms existing in the formerly glaciated environments allows reconstruction of the post-glacial environmental dynamics in the upper Garonne basin. Today, the highest lands are organized following three elevation belts: subnival (1500-1900m), nival (1900-2300m) and periglacial/cryonival (2300-2800m).

Recent regional climate cooling on the Antarctic Peninsula and associated impacts on the cryosphere

The Antarctic Peninsula (AP) is often described as a region with one of the largest warming trends on Earth since the 1950s, based on the temperature trend of 0.54°C/decade during 1951-2011 recorded at Faraday/Vernadsky station. Accordingly, most works describing the evolution of the natural systems in the AP region cite this extreme trend as the underlying cause of their observed changes. However, a recent analysis (Turner et al., 2016) has shown that the regionally stacked temperature record for the last three decades has shifted from a warming trend of 0.32°C/decade during 1979-1997 to a cooling trend of -0.47°C/decade during 1999-2014. While that study focuses on the period 1979-2014, averaging the data over the entire AP region, we here update and re-assess the spatially-distributed temperature trends and inter-decadal variability from 1950 to 2015, using data from ten stations distributed across the AP region. We show that Faraday/Vernadsky warming trend is an extreme case, circa twice those of the long-term records from other parts of the northern AP. Our results also indicate that the cooling initiated in 1998/1999 has been most significant in the N and NE of the AP and the South Shetland Islands (>0.5°C between the two last decades), modest in the Orkney Islands, and absent in the SW of the AP. This recent cooling has already impacted the cryosphere in the northern AP, including slow-down of glacier recession, a shift to surface mass gains of the peripheral glacier and a thinning of the active layer of permafrost in northern AP islands.

On the outside looking in: rethinking the molecular mechanism of 1,3-dipolar cycloadditions from the perspective of bonding evolution theory. The reaction between cyclic nitrones and ethyl acrylate

Understanding the molecular mechanism of 1,3-dipolar cycloadditions using the bonding evolution theory.

A novel group of IncQ1 plasmids conferring multidrug resistance

The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.