Abundance Of Sequences Research Articles

Dual signal amplification-integrated single-molecule biosensing of flap endonuclease 1 in breast cancer tissues

Flap endonuclease 1 (FEN1) is a structure-specific nuclease that may act as a valuable biomarker for cancer diagnosis. Herein, we construct a dual signal amplification-integrated single-molecule fluorescent biosensor for ultrasensitive detection of FEN1 in breast cancer tissues. We design a triplex DNA containing a flap structure for both recognizing and amplifying FEN1 signal. When FEN1 is present, flap is specifically cleaved by FEN1 and released from triplex DNA to form a short ssDNA strand with free 3' OH terminus, and the resultant ssDNA can serve as the primer and binds to circular template in triplex DNA to trigger rolling circle amplification (RCA), generating a long ssDNA product with abundant repeated activator sequences. The hybridization of the resultant activators with crRNAs subsequently activates Cas12a to catalyze trans-cleavage of Cy5- and BHQ-labeled probes to restore Cy5 fluorescence that can be quantified by single-molecule detection. Notably, only a single triplex DNA is required for both initiating and implementing RCA, greatly simplifying the reaction system and eliminating nonspecific amplification. This biosensor exhibits ultrahigh sensitivity with a detection limit of 2.24 × 10-5 U/μL, facilitating accurate detection of endogenous FEN1 activity with single-cell sensitivity and discrimination of different FEN1 levels in clinical breast cancer tissues.

Bacterial and Fungal Community Profiling of Karst Ecosystem in Basey, Samar, Philippines Using Shotgun Metagenomic Approach

The Philippines has an abundance of karst or forest over limestone landscapes, but only a small percentage of them have been studied and protected. Although the flora and fauna of karst forests are diverse and unique, little is known about the microflora that inhabits this ecosystem. The taxonomic and functional composition of bacteria and fungi in soil samples from three locations within three karst forest zones in Basey, Samar, Philippines were analyzed using Illumina shotgun metagenome sequencing. Proteobacteria and Actinobacteria bacterial sequences were most prevalent in the karst soil, followed by those of the Firmicutes, Acidobacteria, Chloroflexi, Planctomycetes, Cyanobacteria, Verrumicrobia, Bacteriodetes, and Deinococcus-Thermus. The most abundant fungal sequences belonged to Ascomycota, followed by Basidiomycota. An average of 33 million predicted protein features was detected across all sites. Enzyme pathways for nitrogen and sulfur metabolism, and several carbon fixation pathways, appeared nearly complete. To our knowledge, this is the first report to provide baseline information on the microbial community and their possible roles in karst forest ecosystem health in the Philippines, which may lead to identifying new microbes with specialized metabolism and promoting biodiversity conservation of karst forests in the Philippines. Furthermore, correlation analysis with plant diversity will reveal plant-microbe interaction leading to the understanding of the adaptation, abundance, survival, and diversity of microorganisms and plants.

Prevalent fingerprint of marine macroalgae in arctic surface sediments

Macroalgal forests export much of their production, partly supporting food webs and carbon stocks beyond their habitat, but evidence of their contribution in sediment carbon stocks is poor. We test the hypothesis that macroalgae contribute to carbon stocks in arctic marine sediments. We used environmental DNA (eDNA) fingerprinting on a large-scale set of surface sediment samples from Greenland and Svalbard. We evaluated eDNA results by comparing with traditional survey and tracer methods. The eDNA-based survey identified macroalgae in 94 % of the sediment samples covering shallow nearshore areas to 1460 m depth and 350 km offshore, with highest sequence abundance nearshore and with dominance of brown macroalgae. Overall, the eDNA results reflected the potential source communities of macroalgae and eelgrass assessed by traditional surveys, with the most abundant orders being common among different methods. A stable isotope analysis showed a considerable contribution from macroalgae in sediments although with high uncertainty, highlighting eDNA as a great improvement and supplement for documenting macroalgae as a contributor to sediment carbon stocks. Conclusively, we provide evidence for a prevalent contribution of macroalgal forests in arctic surface sediments, nearshore as well as offshore, identifying brown algae as main contributors.

A decade of microbial community dynamics on sinking particles during high carbon export events in the eastern Fram Strait

Marine sinking particles sequester atmospheric carbon dioxide to the deep ocean via the biological carbon pump. Understanding how environmental shifts drive changes in the microbial composition of particles, and how these affect the export of organic matter from the surface to the deep ocean, is critical, especially in the rapidly changing Arctic Ocean. Here, we applied next generation sequencing of the 18S and 16S rRNA genes to sediment trap samples from around 200 m water depth in the eastern Fram Strait, covering a time frame of more than one decade (2000-2012). The aim was to characterize their microbial composition during annual highest particulate organic carbon flux events. The bimodal annual spring and summer export fluxes were representative of the strong seasonality in the region. Furthermore, the study period was characterized by considerable interannual variation, marked especially by a warm water anomaly between 2005 and 2007. During this period changes in the hydrography and sea ice cover also led to measurable changes in the microbial composition of particles. The warm water period was marked by a decrease in diatoms affiliated with Chaetoceros, an increase of small phytoplankton and an increase in sequence abundance of the bacterial taxa Oceanospirillales, Alteromonadales and Rhodobacterales on the particles. The resulting changes in microbial composition and the associated microbial network structure suggest the emergence of a more developed retention system in the surface ocean. Our results provide the first long-term assessment of the microbial composition of sinking particles in the Arctic Ocean, and stress the importance of sea ice and hydrography for particle composition and subsequent flux of organic matter to deeper waters.

Comparative genomics reveals insights into anuran genome size evolution

BackgroundAmphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types.ResultsOur results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats.ConclusionsOverall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.

A microcystin synthesis mcyE/ndaF gene assay enables early detection of microcystin production in a tropical wastewater pond

Cyanobacteria can dominate the algal community in wastewater ponds, which can lead to the production of cyanotoxins and their release into the environment. We applied traditional and molecular techniques to identify cyanotoxin hazards and high-risk periods in a tropical wastewater treatment system. Potentially toxic cyanobacteria were identified by microscopy and amplicon sequencing over the course of a year. Toxin gene levels were monitored and compared to toxin production to identify likely toxin producing species and high-risk periods. Cyanobacteria were persistent in the effluent year-round, with Planktothrix and Microcystis the most abundant genera; Microcystis could not be resolved beyond genus using amplicon sequencing, but M. flos-aquae was identified as a dominant species by microscopy. Microcystin toxin was detected for the first time in treated effluent at the beginning of the wet season (December 2018), which correlated with an increase in Microcystis amplicon sequence abundance and elevated microcystin toxin gene (mcyE/ndaF) levels. Concomitantly, microscopy data showed an increase in M. flos-aquae but not M. aeruginosa. These data informed a refined sampling campaign in 2019 and results showed a strong correlation between mcyE/ndaF gene abundance, microcystin toxin levels and Microcystis amplicon sequence abundance. Microscopy data showed that in addition to M. flos-aquae, M. aeruginosa was also abundant in February and March 2019, with highest levels coinciding with toxin detection and toxin gene levels. M. aeruginosa was the most abundant Microcystis species detected in selected treated effluent samples by metagenomics analysis, and elevated levels coincided with toxin production. All microcystin genes in the biosynthesis pathway were detected, but microcystin genes from Planktothrix agardhii were not detected.Gene toxin assays were successfully used to predict microcystin production in this wastewater system. Changes in amplicon sequence relative abundance were a useful indicator of changes in the cyanobacterial community. We found that metagenomics was useful not just for identifying the most abundant Microcystis species, but the detection of microcystin biosynthesis genes helped confirm this genus as the most likely toxin producer in this system. We recommend toxin gene testing for the early detection of potential toxin producing cyanobacteria to manage the risk of toxicity and allow the implementation of risk management strategies.

Seasonal Dynamics of Marine Bacterial Communities in Aquaculture Farms: The case of the Northern Ionian Coastal Ecosystem (Mediterranean Sea)

Coastal aquaculture systems are complex environments with multiple microbial interactions that affect fish health and productivity. High-throughput amplicon sequencing is a valuable tool for identifying such bacterial communities and investigating the relationship between bacterial diversity and sustainability in these systems. In the present study, the seasonal dynamics of marine bacterial communities were assessed, in terms of diversity and composition, in three marine aquaculture farms in the northern Ionian Sea (western Greece) and a distant control site unaffected by aquaculture activities, using 16S rRNA amplicon metabarcoding. Results revealed that Proteobacteria, Bacteroidota, Cyanobacteria, and Verrucomicrobiota were the dominant phyla in the bacterial communities. Alpha diversity was significantly lower in the aquaculture farms compared to the control site. Season was the major factor driving bacterial community fluctuations. Comparative analysis between seasons revealed the presence of differentially abundant amplicon sequence variants (ASVs) in all pairwise comparisons, with the majority of them belonging to the phyla Bacteroidota (families Flavobacteriaceae, Cryomorphaceae) and Proteobacteria (family Rhodobacteraceae). Our study provides the first detailed description of bacterial communities present in Greek coastal aquaculture farms using amplicon metabarcoding analysis and expands our understanding of the impact of seasonality and environmental variables on marine bacterial community diversity and composition.

Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus Gossypium, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes.

Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.

Incomplete recovery of gut microbiota in marine medaka (Oryzias melastigma) during the depuration phase, after exposure to sulfamethazine/nanoplastics

The persistence of antibiotics and nanoplastics in aquatic environment poses a great threat to aquatic organisms. In our previous study, significant decreases of bacterial richness and changes of bacterial communities in the Oryzias melastigma gut after sulfamethazine (SMZ) and polystyrene nanoplastics (PS) exposure were observed. Here, the O. melastigma dietary exposed to SMZ (0.5 mg/g, LSMZ; 5 mg/g, HSMZ), PS (5 mg/g, PS) or PS + HSMZ were depurated for 21 days to assess the extent of which these effects were reversible. Our results revealed that most diversity indexes of bacterial microbiota in the O. melastigma gut from the treatment groups were insignificantly different from the control, suggesting a large recovery of bacterial richness. Although the sequence abundances of a few genera remained significantly changed, the proportion of dominant genus was recovered. Exposure to SMZ affected the complexity of the bacterial networks, and the cooperation and exchange events of positively associated bacteria were enhanced during this period. After depuration, increases in the complexity of networks and intense competitions among bacteria were observed, which was beneficial for the robustness of networks. However, the gut bacterial microbiota was less stable, and several functional pathways were dysregulated, relative to the control. In addition, higher occurrence of pathogenic bacteria was found in the PS + HSMZ group relative to the signal pollutant group after depuration, indicating a greater hazard for the mixture of PS and SMZ. Taken together, this study contributes to a better understanding of the recovery of bacterial microbiota in fish gut after individual and combined exposure to nanoplastics and antibiotics.

Detecting fecal microbiota transplantation–associated infection transmission using shotgun metagenomic sequencing and clonality analysis

Background: Fecal microbiota transplantation (FMT) is a widely used modality for safe and effective treatment of recurrent Clostridium difficile infections, and FMT is being explored for the treatment of additional indications including gastrointestinal diseases and neurological disorders. Although microbiota-based therapies like FMT utilize rigorous donor screening procedures, these procedures are limited in resolution and scope, and there remains a risk of transmission of FMT-associated infectious agents from donor stool to a FMT recipient. Critically, these health concerns led the FDA to issue a 2019 safety alert for the transmission risks associated with FMT and to update its guidelines for screening and reporting. In a suspected transmission event, there is uncertainty around the source of infection; thus, methods are needed to rapidly determine whether a patient’s infection is linked to the donor stool product. Methods: Here, we developed a laboratory service sequencing and bioinformatics pipeline within our CLIA-certified laboratory for investigating suspected FMT infection transmission by measuring genomic relatedness. Our pipeline performs deep sequencing of a metagenomic sample, whole-genome sequencing (WGS) of an isolate derived from the implicated patient infection and determines the genomic relatedness between the 2 using a SNP-based analysis. The workflow was validated in silico with synthetic metagenomic samples spiked-in with WGS of clinically relevant isolate strains at varying abundance. Results: The sample and sequencing library preparation workflow was optimized across a panel of metagenomic and mock fecal microbiome samples demonstrating reproducible and reduced-bias sequencing of metagenomic samples. Our pipeline demonstrates high sensitivity and specificity for clonality calls when a spiked in isolate genome achieves 5× depth for >50% of the genome. We also demonstrated an interplay between abundance rate and sequencing depth for determining a clonality limit of detection. Conclusions: Taken together, our pipeline represents a new method that can support the clinical efforts of FMT and other microbiota-based therapies.

Comprehensive analysis of the complete mitochondrial genomes of three Coptis species (C. chinensis, C. deltoidea and C. omeiensis): the important medicinal plants in China.

Coptis plants (Ranunculaceae) contain high levels of isoquinoline alkaloids and have a long history of medicinal use. Coptis species are of great value in pharmaceutical industries and scientific research. Mitochondria are considered as one of the central units for receiving stress signals and arranging immediate responses. Comprehensive characterizations of plant mitogenomes are imperative for revealing the relationship between mitochondria, elucidating biological functions of mitochondria and understanding the environmental adaptation mechanisms of plants. Here, the mitochondrial genomes of C. chinensis, C. deltoidea and C. omeiensis were assembled through the Nanopore and Illumina sequencing platform for the first time. The genome organization, gene number, RNA editing sites, repeat sequences, gene migration from chloroplast to mitochondria were compared. The mitogenomes of C. chinensis, C. deltoidea and C. omeiensis have six, two, two circular-mapping molecules with the total length of 1,425,403 bp, 1,520,338 bp and 1,152,812 bp, respectively. The complete mitogenomes harbors 68-86 predicted functional genes including 39-51 PCGs, 26-35 tRNAs and 2-5 rRNAs. C. deltoidea mitogenome host the most abundant repeat sequences, while C. chinensis mitogenome has the largest number of transferred fragments from its chloroplasts. The large repeat sequences and foreign sequences in the mitochondrial genomes of Coptis species were related to substantial rearrangements, changes in relative position of genes and multiple copy genes. Further comparative analysis illustrated that the PCGs under selected pressure in mitochondrial genomes of the three Coptis species mainly belong to the mitochondrial complex I (NADH dehydrogenase). Heat stress adversely affected the mitochondrial complex I and V, antioxidant enzyme system, ROS accumulation and ATP production of the three Coptis species. The activation of antioxidant enzymes, increase of T-AOC and maintenance of low ROS accumulation in C. chinensis under heat stress were suggested as the factors for its thermal acclimation and normal growth at lower altitudes. This study provides comprehensive information on the Coptis mitogenomes and is of great importance to elucidate the mitochondrial functions, understand the different thermal acclimation mechanisms of Coptis plants, and breed heat-tolerant varieties.

Community structure of zooplankton and its response to aquatic environmental changes based on eDNA metabarcoding

Environmental DNA (eDNA), as a tool for rapid, non-invasive biodiversity monitoring and ecological assessment, is pivotal to the understanding of aquatic biodiversity. In this study, eDNA metabarcoding technology was compared with conventional microscopical approaches to identify the variability characteristics of Weihe River community structure under changing environment. The number of species identified by molecular method was 3 times that by traditional method, which significantly improved the identification ability of species. There was a positive correlation between sequence abundances and microscopical individual counts (r = 0.84, p < 0.05；r = 0.97, p < 0.05). COI gene markers were more discriminative for the biological communities' heterogeneity, and their first two principal components (PC1 and PC2) explained 55.54% of the variance of the total variables. Moreover, molecular methods elucidated the interaction between eco-hydrological variables and zooplankton community structure. The variation of land-use types led to significant differences in zooplankton abundance. Total nitrogen, Water temperature, river width and altitudewere the key impact factors of zooplankton community change (p < 0.01). We believe that our research would provide meaningful demos on the application of eDNA technology in river ecosystem monitoring and assessment.

Butanol as a major product during ethanol and acetate chain elongation.

Chain elongation is a relevant bioprocess in support of a circular economy as it can use a variety of organic feedstocks for production of valuable short and medium chain carboxylates, such as butyrate (C4), caproate (C6), and caprylate (C8). Alcohols, including the biofuel, butanol (C4), can also be generated in chain elongation but the bioreactor conditions that favor butanol production are mainly unknown. In this study we investigated production of butanol (and its precursor butyrate) during ethanol and acetate chain elongation. We used semi-batch bioreactors (0.16L serum bottles) fed with a range of ethanol concentrations (100-800mM C), a constant concentration of acetate (50mM C), and an initial total gas pressure of ∼112kPa. We showed that the butanol concentration was positively correlated with the ethanol concentration provided (up to 400mM C ethanol) and to chain elongation activity, which produced H2 and further increased the total gas pressure. In bioreactors fed with 400mM C ethanol and 50mM C acetate, a concentration of 114.96 ± 9.26mM C butanol (∼2.13gL-1) was achieved after five semi-batch cycles at a total pressure of ∼170kPa and H2 partial pressure of ∼67kPa. Bioreactors with 400mM C ethanol and 50mM C acetate also yielded a butanol to butyrate molar ratio of 1:1. At the beginning of cycle 8, the total gas pressure was intentionally decreased to ∼112kPa to test the dependency of butanol production on total pressure and H2 partial pressure. The reduction in total pressure decreased the molar ratio of butanol to butyrate to 1:2 and jolted H2 production out of an apparent stall. Clostridium kluyveri (previously shown to produce butyrate and butanol) and Alistipes (previously linked with butyrate production) were abundant amplicon sequence variants in the bioreactors during the experimental phases, suggesting the microbiome was resilient against changes in bioreactor conditions. The results from this study clearly demonstrate the potential of ethanol and acetate-based chain elongation to yield butanol as a major product. This study also supports the dependency of butanol production on limiting acetate and on high total gas and H2 partial pressures.

Development of STARP Marker Platform for Flexible SNP Genotyping in Sugarbeet

Single nucleotide polymorphisms (SNPs) have been widely used for gene identification. Allelic discrimination for an individual SNP with high reliability and flexibility is critical for the accurate detection of beneficial genes linked to specific SNP sites. Several SNP genotyping platforms have been developed but most exclusively rely on fluorescence signals for allelic differentiation. Genotyping via a fluorescence signal can have a lower accuracy if strong background signal noise is present, a common challenge associated with crop genetics. The semi-thermal asymmetric reverse PCR (STARP) marker system introduces extra SNPs in its forward primers to ensure specificity of the PCR reaction and adds a 4-nucleotide insertion into one universal primer to create fragment length polymorphism among STARP markers, which makes SNP allelic discrimination possible through either fluorescence signals or traditional gel electrophoresis. The STARP marker system is preferable for SNP genotyping in crops such as sugarbeet (Beta vulgaris ssp. Vulgaris L.) that exhibit strong background signal noise during PCR reactions due to an abundant repetitive sequence and high levels of heterozygosity in the genome. In this study, SNPs among sugarbeet lines were detected through genotype-by-sequencing (GBS) and confirmed by sequencing PCR products containing SNP sites. STARP primers were designed, and they generated STARP markers clearly discriminated by SNP alleles among sugarbeet plants either through a fluorescence signal or fragment length polymorphism. In addition, by prolonging 5-nucleotide in an allele-specific forward primer F2 that increased fragment length polymorphism of STARP markers from 4-bp to 9-bp, genotyping individual SNPs can be performed using user-friendly agarose gels. This research resulted in the development of a STARP marker platform for the flexible genotyping of individual SNPs of sugarbeet as well as an improved STARP technique for easy SNP allelic discrimination that also has utilities in other plant species.

Corn-Based Fluorescent Light-Up Biosensors with Improved Signal-to-Background Ratio for Label-Free Detection of Long Noncoding RNAs.

Long noncoding RNAs (lncRNAs) play pivotal roles in multifarious physiological and pathological processes, and their aberrant expression may disturb the normal regulatory network of gene expression to induce diverse human diseases. Herein, we construct a fluorescent light-up biosensor with a low background for label-free detection of lncRNAs by coupling duplex-specific nuclease (DSN)-assisted target recycling amplification with transcription-driven synthesis of fluorogenic RNA aptamer-Corns. We design two linear probes, including a capture probe for initiating a cyclic cleavage reaction and a linear template for transcribing RNA aptamer-Corn. Target lncRNA is recognized by capture probes assembled on magnetic bead (MB) surfaces to trigger a DSN-assisted cyclic cleavage reaction, releasing abundant T7 promoter sequences. After magnetic separation, free T7 promoter hybridizes with a linear template to induce efficient transcription amplification with the assistance of T7 RNA polymerase, producing numerous fluorogenic RNA aptamer-Corns that can light up small-molecule fluorogens 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO). Notably, the introduction of MBs facilitates both the separation of cleaved capture probes and the enrichment/isolation of target lncRNAs from the complex biological matrix. Benefiting from the high efficiency of DSN/T7 RNA polymerase-mediated cascade amplification and high signal-to-background ratio of the Corn-DFHO complex, this biosensor is capable of sensitively quantifying lncRNA with a detection limit of 31.98 aM. Moreover, it can precisely quantify lncRNA at the single-cell level and even in complex biological samples, and it can differentiate tumor cells from normal cells. Importantly, this Corn-based biosensor is readily extended to detect other lncRNAs by altering capture probe sequences, opening a new avenue for molecular diagnosis.

Hydrogeochemical characterisation and geospatial analysis of groundwater for drinking water quality in Ludhiana district of Punjab, India

This study characterises the quality of groundwater for the Ludhiana district of Punjab, India by analysing water samples collected from 152 locations spread across 3767 km2. The samples were analysed for 18 parameters consisting of pH, EC, TDS, TA, TH, major anions and cations. The parameter values have been used to calculate the drinking water quality index of the study area which suggests that 2.6, 57.9, 32.9, 4 and 2.6% of the samples fall under the excellent, good, poor, very poor and unsuitable categories, respectively. The sequence of abundance for ions (in meq/l) as revealed from the laboratory tests is Na+ (37.1%) > Ca2+ (30.8%) > Mg2+ (29.1%) > K+ (2.8%) for cations and HCO3- (80%) > Cl¯ (8.9%) > CO32- (6.5%) > SO42- (3.9%) > NO3-, F-, PO43- (< 1%) for anions. The spatial variability of these parameters has been depicted through the use of interpolation maps. Evaluation of different ionic ratios indicates that carbonate weathering and silicate weathering are both significantly affecting the groundwater chemistry with a slight dominance of carbonate weathering. Also, the ion exchange process is taking place in the area as confirmed by CAI index values. In terms of saturation index, the groundwater is undersaturated with respect to halite, fluorite and sylvite, whereas it is supersaturated for calcite, dolomite and aragonite minerals. The principal components in PCA explained 75.4% of the total variance with 29.1 and 28.3% contributions from PC1 and PC2. Both of these components indicate towards the geogenic and anthropogenic influence on groundwater mineralization of the area. The analysis suggests that groundwater for the study area is suitable for drinking in most of the region expect in a few places. Such a study could be used to understand the current status of groundwater quality in the area, the results of which can be used to prevent further contamination and sustain the resource for the future.

A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction.

Protein function prediction is a major challenge in the field of bioinformatics which aims at predicting the functions performed by a known protein. Many protein data forms like protein sequences, protein structures, protein-protein interaction networks, and micro-array data representations are being used to predict functions. During the past few decades, abundant protein sequence data has been generated using high throughput techniques making them a suitable candidate for predicting protein functions using deep learning techniques. Many such advanced techniques have been proposed so far. It becomes necessary to comprehend all these works in a survey to provide a systematic view of all the techniques along with the chronology in which the techniques have advanced. This survey provides comprehensive details of the latest methodologies, their pros and cons as well as predictive accuracy, and a new direction in terms of interpretability of the predictive models needed to be ventured by protein function prediction systems.

Specific Intratumor Bacteria Genera and TRG Recombinations Associated with Greater Survival Probability in Alimentary Tract Cancers.

There remains a lack of knowledge regarding the effects of the intratumor microbiome on the tumor immune milieu. We aimed to investigate whether intratumoral bacterial RNA sequence abundance in gastric and esophageal cancers is associated with T-cell infiltrate features. We assessed cases representing the stomach adenocarcinoma (STAD) and esophageal cancer (ESCA) databases of The Cancer Genome Atlas. RNA-seq data estimating intratumoral bacterial abundance was obtained from publicly available sources. TCR recombination reads were mined from exome files. Survival models were generated using the lifelines python package. Increasing levels of the Klebsiella genus were associated with a better OS probability (hazard ratio, 0.5), via a Cox proportional hazards model. The higher Klebsiella abundance was associated with a significantly increased overall (p = 0.0001) and disease-specific survival (p = 0.0289) probability for the STAD dataset. Cases representing the upper 50th percentile of Klebsiella abundance also represented a significantly increased recovery of TRG and TRD recombination reads (p = 0.00192). Analogous results were found for the Aquincola genus in ESCA. This is the first report of associations between low biomass bacterial samples from primary tumor samples with patient survival and with an increased gamma-delta T cell infiltrate. Results indicate that the gamma-delta T cells potentially play a role in the dynamics of the bacterial infiltration of primary tumors of the alimentary tract.

Isolation and Characteristics of a Novel Aichivirus D from Yak.

Aichivirus D (AiV-D) is a newly emerging Kobuvirus detected in bovine and sheep, and information is limited regarding its biological significance and prevalence. This study aimed to explore both the prevalence and characteristics of AiV-D in yaks. From May to August 2021, 117 fecal samples were collected from yaks with diarrhea in three provinces of China's Qinghai-Tibet Plateau, 15 of which were selected and pooled for metagenomic analysis. A high abundance of AiV-D sequences was obtained. Of the 117 diarrhea samples, 29 (24.8%) tested AiV-D-positive, including 33.3% (14/42) from Sichuan, 21.1% (8/38) from Qinghai, and 18.9% (7/37) from Tibet, respectively, suggesting a wide geographical distribution of the AiV-D in yaks in the Qinghai-Tibet Plateau. Furthermore, three AiV-D strains were successfully isolated using Vero cells. Significantly, the AiV-D strain could cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, duodenum, colon, cecum, and rectum. Based on phylogenetic analysis of the genome and capsid protein P1 (VP0, VP3, and VP1 genes), the yak AiV-D strains likely represent a novel genotype of AiV-D. On the whole, this study identified a novel genotype of AiV-D from yaks, which was successfully isolated, and confirmed that this virus is a diarrhea pathogen in yaks and has a wide geographical distribution in the Qinghai-Tibet Plateau. Our results expand the host range of AiV-D and the pathogen spectrum of yaks and have significant implications for diagnosing and controlling diarrhea in yaks. IMPORTANCE In this study, we identified and successfully isolated a novel genotype of AiV-D from yaks. Animal infection confirmed that this virus can cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, cecum, duodenum, colon, and rectum. All of these results have significant implications for diagnosing and controlling diarrhea in yaks. These novel AiV-D strains have a wide geographical distribution in yaks from the Qinghai-Tibet Plateau in China. In addition to expanding the host range of AiV-D and the pathogen spectrum of yaks, these findings can increase knowledge of the prevalence and diversity of AiV-D.