Related Sequences Research Articles

Gut microbiota profiles in two New Zealand cohorts with overweight and prediabetes: a Tū Ora/PREVIEW comparative study.

Obesity-related metabolic diseases such as type 2 diabetes (T2D) are major global health issues, affecting hundreds of millions of people worldwide. The underlying factors are both diverse and complex, incorporating biological as well as cultural considerations. A role for ethnicity - a measure of self-perceived cultural affiliation which encompasses diet, lifestyle and genetic components - in susceptibility to metabolic diseases such as T2D is well established. For example, Asian populations may be disproportionally affected by the adverse 'TOFI' (Thin on the Outside, Fat on the Inside) profile, whereby outwardly lean individuals have increased susceptibility due to excess visceral and ectopic organ fat deposition. A potential link between the gut microbiota and metabolic disease has more recently come under consideration, yet our understanding of the interplay between ethnicity, the microbiota and T2D remains incomplete. We present here a 16S rRNA gene-based comparison of the fecal microbiota of European-ancestry and Chinese-ancestry cohorts with overweight and prediabetes, residing in New Zealand. The cohorts were matched for mean fasting plasma glucose (FPG: mean ± SD, European-ancestry: 6.1 ± 0.4; Chinese-ancestry: 6.0 ± 0.4 mmol/L), a consequence of which was a significantly higher mean body mass index in the European group (BMI: European-ancestry: 37.4 ± 6.8; Chinese-ancestry: 27.7 ± 4.0 kg/m2; p < 0.001). Our findings reveal significant microbiota differences between the two ethnicities, though we cannot determine the underpinning factors. In both cohorts Firmicutes was by far the dominant bacterial phylum (European-ancestry: 93.4 ± 5.5%; Chinese-ancestry: 79.6 ± 10.4% of 16S rRNA gene sequences), with Bacteroidetes and Actinobacteria the next most abundant. Among the more abundant (≥1% overall relative sequence abundance) genus-level taxa, four zero-radius operational taxonomic units (zOTUs) were significantly higher in the European-ancestry cohort, namely members of the Subdoligranulum, Blautia, Ruminoclostridium, and Dorea genera. Differential abundance analysis further identified a number of additional zOTUs to be disproportionately overrepresented across the two ethnicities, with the majority of taxa exhibiting a higher abundance in the Chinese-ancestry cohort. Our findings underscore a potential influence of ethnicity on gut microbiota composition in the context of individuals with overweight and prediabetes.

A novel family of sugar-specific phosphodiesterases that remove zwitterionic modifications of GlcNAc

The zwitterions phosphorylcholine (PC) and phosphoethanolamine (PE) are often found esterified to certain sugars in polysaccharides and glycoconjugates in a wide range of biological species. One such modification involves PC attachment to the 6-carbon of N-acetylglucosamine (GlcNAc-6-PC) in N-glycans and glycosphingolipids (GSLs) of parasitic nematodes, a modification that helps the parasite evade host immunity. Knowledge of enzymes involved in the synthesis and degradation of PC and PE modifications is limited. More detailed studies on such enzymes would contribute to a better understanding of the function of PC modifications and have potential application in the structural analysis of zwitterion-modified glycans. In this study, we used functional metagenomic screening to identify phosphodiesterases encoded in a human fecal DNA fosmid library that remove PC from GlcNAc-6-PC. A novel bacterial phosphodiesterase was identified and biochemically characterized. This enzyme (termed GlcNAc-PDase) shows remarkable substrate preference for GlcNAc-6-PC and GlcNAc-6-PE, with little or no activity on other zwitterion-modified hexoses. The identified GlcNAc-PDase protein sequence is a member of the large endonuclease/exonuclease/phosphatase superfamily where it defines a distinct subfamily of related sequences of previously unknown function, mostly from Clostridium bacteria species. Finally, we demonstrate use of GlcNAc-PDase to confirm the presence of GlcNAc-6-PC in N-glycans and GSLs of the parasitic nematode Brugia malayi in a glycoanalytical workflow.

Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding.

Fish diversity plays a critical role in maintaining the balance of water ecosystems, especially in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes in the upper Yangtze River, which serves as an important habitat for rare and endemic fish, as well as an important channel for the replenishment of fishery resources in the Three Gorges Reservoir. Under a 10-year ban on fishing in the Yangtze River basin, we investigate fish diversity and seasonal variation in the Reserve by using environmental DNA (eDNA) metabarcoding. We found fishes belonging to 85 genera, 24 families, and 8 orders in the Reserve. A comparison of eDNA metabarcoding results with the diversity of a recent fish catch revealed that eDNA metabarcoding not only enables rapid and efficient fish monitoring but also has a high sensitivity. Furthermore, the study demonstrates that eDNA metabarcoding can be used as a tool for monitoring seasonal variations of fish composition in freshwater ecosystems. The alpha and beta diversity analysis both showed compositional differences in the fish community in accordance with seasonal variations. In addition, changes in eDNA relative sequence abundance and the detection of fish species at different sampling sites may reflect shifts in habitat use and distribution. Thus, we provide detailed seasonal data on fish diversity in the Chongqing section of the Reserve. This will contribute to conservation and to the understanding of fish diversity and community dynamics in the Chongqing section of the Reserve.

Pseudomonas hormoni sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada.

Bacterial strain G20-18T was previously isolated from the rhizosphere of an Arctic grass on Ellesmere Island, Canada and was characterized and described as Pseudomonas fluorescens. However, new polyphasic analyses coupled with phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 5-25 °C (optimum, 20-25 °C), at pH 5-9 (optimum, pH 6-7) and with 0-4 % NaCl (optimum, 2 % NaCl). The major fatty acids are C16 : 0 (35.6 %), C17 : 0 cyclo ω7c (26.3 %) and summed feature C18 : 1/C18 : 1 ω7c (13.6 %). The respiratory quinones were determined to be Q9 (93.5 %) and Q8 (6.5 %) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain G20-18T was shown to synthesize cytokinin and auxin plant hormones and to produce 1-aminocyclopropane-1-carboxylate deaminase. The DNA G+C content was determined to be 59.1 mol%. Phylogenetic analysis based on the 16S rRNA gene and multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) showed that G20-18T was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas. Comparisons of the G20-18T genome sequence and related Pseudomonas type strain sequences showed an average nucleotide identity value of ≤93.6 % and a digital DNA-DNA hybridization value of less than 54.4 % relatedness. The phenotypic, phylogenetic and genomic data support the hypothesis that strain G20-18T represents a novel species of the genus Pseudomonas. As strain G20-18T produces or modifies hormones, the name Pseudomonas hormoni sp. nov. is proposed. The type strain is G20-18T (=LMG 33086T=NCIMB 15469T).

Prevalence and molecular identification of gastrointestinal nematodes in Qinghai-Tibetan Plateau of China.

Gastrointestinal nematodes (GINs) have seriously affected the production and earnings of animal husbandry in various countries, while some species of GINs infect humans. At present, little is known about the species and prevalence of GINs in Qinghai-Tibetan Plateau (QTP). In this study, 528 fresh faecal samples were collected from typical areas in different altitudes with seven species of livestock in Qinghai, Tibet, Gansu and Yunnan Provinces. ITS-2 rRNA gene of nematodes was employed to detect by PCR and sequencing analysis. Phylogenetic analysis of related sequences was performed using MEGA 6.0 software. The overall prevalence of GINs was 80.3% with 20 species of GINs detected, while Teladorsagia circumcincta was the dominant one, and four of which were zoonotic species such as Trichostrongylus colubriformis, Trichostrongylus axei, Trichostrongylus vitrinus and Oesophagostomum stephanostomum. The study provided panoptic information on the prevalence and species diversity of GINs in QTP area, which is useful and valuable for reference of measure formulation in livestock husbandry and public health concerns. The parasites of T. circumcincta, Cylicocyclus nassatus, Strongylus edentatus, Cylicostephanus longibursatus, Telephlebia brevicauda, Cyathostomum catinatum, Mecistocirrus digitatus, Cooperia punctata, Cylicodontophorus bicoronatus, Nematodirus oiratianus and Oesophagostomum asperum were firstly reported the presence in QTP area. The study also showed that horse could be infected by T. circumcincta, goat could be infected by C. nassatus, cattle could be infected by S. edentatus and C. bicoronatus,and O. stephanostomum could infect yak, cattle and Mongolian sheep in worldwide. Nevertheless, more investigations are needed, such as microscopic examination, to accurately determine the species in the region.

DNA i‐motif formation at physiological pH revealed by Raman spectroscopy

AbstractThe intercalated motif (iM) is a four‐stranded structure consisting of two parallel homoduplexes formed by hemiprotonated C.C+ pairs and intercalated antiparallel to each other. iM is generally formed at acidic pH, as cytosine protonation is required for its formation. However, sequences with long cytosine tracts can form iM at physiological pH conditions. Here, we use both off‐resonant Raman and UV‐resonant Raman (using synchrotron radiation) spectroscopy (RS) to study the sequence (C9T3)3C9, which has been recently thoroughly analysed by other spectroscopic methods (CD, 1H NMR). In line with these methods, RS has shown that (C9T3)3C9 adopts iM at neutral pH and the iM forms with slow kinetics, melts in multiple steps and exhibits a large thermal hysteresis between the folding and refolding processes. The presence of isosbestic points in the temperature‐dependent Raman spectra (in line with the SVD analysis indicating just two independent spectral components) suggests that the (C9T3)3C9 is found as a mixture of disordered and ordered structures, the proportion of which is temperature dependent. The ordered iM species are believed to be composed of the same type of C.C+ pairs but differing in their number and arrangement along the cytosine tracts. The related sequence (C9A3)3C9 shows the same behaviour as (C9T3)3C9, indicating that the substitution of adenine bases for thymine bases has little effect.

Three-dimensional tilings of blocks and bracelets and related {2,1,2} sequences

This paper discusses the combinatorial interpretation of the H_n numbers, where each Hn denotes the number of ways to tile a 2 2 n block with 2 2 1 plates and 6-block L shapes. It then investigates a closely related tiling sequence, which is tiling a 22n bracelet with the same two building blocks, and discusses its relation with Hn. The recursive equation for both integer sequences are found using one to one correspondence, induction and Newtons Sum. Additionally, in the case of H_n numbers, its related Lucas Style sequence P_n is found. The relationship between the P_n numbers, the Bn numbers and the Hn numbers is similar to that of the Lucas numbers and the Fibonacci numbers. Finally, identities concerning H_ns generating function and its relations with other existing {2,1,2} sequences are discussed, and a theorem that generalizes the generating function of all tiling sequences is proposed and proved.

Marine Cold Seeps As A Gateway Of Deep Subsurface Extremophiles To The Seafloor

In the Earth’s deep subsurface life is comprised exclusively of microorganisms, and estimates indicate 12-45% of the global prokaryotic biomass, on the order of 1029 microbes, is found in subseafloor sediments. Investigating how this enormous microbial biomass is maintained in the extreme habitats below seafloor is critical for understanding the rules of life in the deep biosphere. Furthermore, Earth’s subseafloor habitats often present analog environments detected in other planets such as the recently discovered “ocean worlds”, i.e., planetary bodies in our solar system which consist of large subsurface oceans including Saturn’s moons Titan and Enceladus and Jupiter’s moon Europa. Therefore, investigating life in and beneath Earth’s oceans remains at the forefront of the current astrobiological research endeavors. Despite the inhospitable nature of the subseafloor sedimentary realm, active microbial populations including bacteria capable of transforming into dormant endospores have been demonstrated to inhabit deeply buried anoxic sediments and oil reservoirs, permeable ocean crust, and around hydrothermal vents. These extreme habitats often remain physically connected to the seafloor by unique geological features such as marine cold seeps that transmit hydrocarbon-rich fluids originating in deep sediment layers. It remains unclear how fluid migration in cold seeps influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. In this study, we addressed this knowledge gap by analyzing over 180 marine surficial sediments from the Gulf of Mexico and the Monterey Bay to assess whether hydrocarbon fluid migration serves as a mechanism for the dispersal of subsurface extremophiles and their introduction into the seabed via cold seeps. Seafloor samples were collected either by piston coring or ROV-operated push coring and were stored at -20°C upon collection. Presence of hydrocarbons in the piston core sediments wa characterized by gas chromatography mass spectrometry and fluorescence spectroscopy whereas gas seepage was determined in the ROV push cores by visual confirmation of gas bubbles emanating from the seafloor. Sediment microbiome composition was determined by high throughput 16S rRNA gene amplicon sequencing. Metabolic diversity was assessed via a genome-centric metagenomics approach aided by shotgun metagenomic sequencing of selected samples. Additionally, viable bacterial endospore communities were investigated from a subset of over 120 of the above samples by allowing endospore germination using a high-temperature incubation assay followed by amplicon sequencing. While 132 of the piston core sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the bacterial lineages Atribacterota and Aminicenantia and the archaeal lineage Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of non-respiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. In addition, eight different lineages of anaerobic bacterial endospores activated by sediment incubation assays were strongly associated with hydrocarbon-bearing sediments. These lineages were most closely related to Clostridiales previously detected in oil reservoirs from around the world. These results cumulatively point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.

Sequencing report of the rRNA amplicons of Echinochloa crus-galli in Iraq

This study was conducted to identify the genetic polymorphisms of one wild grass sample species and assess the phylogenetic distribution these isolates occupy based on their internal transcribed (ITS) ribosomal sequences. This study amplified one genetic locus covering a portion of the ITS rRNA sequences. A direct sequencing strategy was performed for the observed PCR amplicons in the amplified genetic locus. Subsequently, a comprehensive phylogenetic tree was constructed in the observed variants for these sequences to reveal the accurate phylogenetic distances alongside other relative sequences. Our results indicated the identity of the investigated wild grass samples (assigned S1 and S2). Sequencing reactions indicated that our investigated samples belonged to Echinochloa crusgalli var. crus-galli (panicum grass), a common wild grass dominated in tropical Asia. Two ribosomal variations were identified in the investigated wild grass samples, 61C&gt;T, observed in the S2 sample and 408C&gt;A, observed in both the S1 and S2 samples. According to the identified results, the investigated samples were positioned within one distinct phylogenetic clade of these identified wild grass sequences in the currently generated comprehensive tree. These positionings were observed within the main clade of Echinochloa crus-galli. Based on the identified ribosomal sequences, it was found that the currently investigated samples may exhibit variable extents of diversities originating from several Asian and South American ancestors. Also, the currently constructed tree revealed that the investigated wild grass sequences belonged to one distinct clade of Echinochloa crus-galli, having many sequences of close phylogenetic connections. This clade occupied far away phylogenetic positions from the other comparable grasses within the same tree. Keywords: rRNA amplicons, Echinochloa crus-galli, Rice

GraphPart: homology partitioning for biological sequence analysis.

When splitting biological sequence data for the development and testing of predictive models, it is necessary to avoid too-closely related pairs of sequences ending up in different partitions. If this is ignored, performance of prediction methods will tend to be overestimated. Several algorithms have been proposed for homology reduction, where sequences are removed until no too-closely related pairs remain. We present GraphPart, an algorithm for homology partitioning that divides the data such that closely related sequences always end up in the same partition, while keeping as many sequences as possible in the dataset. Evaluation of GraphPart on Protein, DNA and RNA datasets shows that it is capable of retaining a larger number of sequences per dataset, while providing homology separation on a par with reduction approaches.

Generalization of procedural motor sequence learning after a single practice trial

When humans begin learning new motor skills, they typically display early rapid performance improvements. It is not well understood how knowledge acquired during this early skill learning period generalizes to new, related skills. Here, we addressed this question by investigating factors influencing generalization of early learning from a skill A to a different, but related skill B. Early skill generalization was tested over four experiments (N = 2095). Subjects successively learned two related motor sequence skills (skills A and B) over different practice schedules. Skill A and B sequences shared ordinal (i.e., matching keypress locations), transitional (i.e., ordered keypress pairs), parsing rule (i.e., distinct sequence events like repeated keypresses that can be used as a breakpoint for segmenting the sequence into smaller units) structures, or possessed no structure similarities. Results showed generalization for shared parsing rule structure between skills A and B after only a single 10-second practice trial of skill A. Manipulating the initial practice exposure to skill A (1 to 12 trials) and inter-practice rest interval (0–30 s) between skills A and B had no impact on parsing rule structure generalization. Furthermore, this generalization was not explained by stronger sensorimotor mapping between individual keypress actions and their symbolic representations. In contrast, learning from skill A did not generalize to skill B during early learning when the sequences shared only ordinal or transitional structure features. These results document sequence structure that can be very rapidly generalized during initial learning to facilitate generalization of skill.

Transformer Graph Convolutional Network for Relative Travel-Time Shift Prediction

Abstract Predicting surface-wave travel-time shifts is valuable for analyzing potential effects caused by changes in medium properties, station clock errors, instrument response errors, and other factors. Many current neural networks used in seismology are single-station models trained using single-station (pair) data. However, most seismic methods require knowledge of the spatial positions between multiple stations. Multiple stations contain rich interrelationships and spatial information that cannot be exploited by single-station models. We proposed a multistation neural network structure Transformer Graph Convolutional Network (TGCN) that utilizes temporal attention and spatial attention to capture spatiotemporal information for predicting relative travel-time shifts. Before that, we introduced a method that treats station pairs as nodes and constructs a graph with multiple station pairs. We collected original ambient noise waveforms from 2017 to 2019 in the Alaska region and 2010 to 2014 in the southern California region to obtain relative travel-time shift sequences of station pairs for model training and testing. To showcase the improvement of spatial information to the model, we compared TGCN with two other baseline single-station models—temporal convolutional network and long short-term memory. Our proposed method predicted travel-time values more accurately than the two baseline models, and it also exhibited slower decay in performance when predicting over larger intervals. We also found that the number of station pairs has an impact on the model. When there are a sufficient number of station pairs, the model can effectively utilize the rich spatial information and achieve higher accuracy. Our approach, which incorporates spatiotemporal information, provides outputs that are more efficient and accurate compared with the traditional single-station (pair) method that only considers temporal information, suggesting that spatial information does enhance the performance of the model.

Discovery of a Novel Cellobiose Dehydrogenase from Cellulomonas palmilytica EW123 and Its Sugar Acids Production.

Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30°C), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 x 105 and 9.06 x 104 (M-1 s-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.

Transposon-encoded nucleases use guide RNAs to promote their selfish spread.

Insertion sequences are compact and pervasive transposable elements found in bacteria, which encode only the genes necessary for their mobilization and maintenance1. IS200- and IS605-family transposons undergo 'peel-and-paste' transposition catalysed by a TnpA transposase2, but they also encode diverse, TnpB- and IscB-family proteins that are evolutionarily related to the CRISPR-associated effectors Cas12 and Cas9, respectively3,4. Recent studies have demonstrated that TnpBand IscB function as RNA-guided DNA endonucleases5,6, but the broader biological role of this activity has remained enigmatic. Here we show that TnpB and IscB are essential to prevent permanent transposon loss as a consequence of the TnpA transposition mechanism. We selected a family of related insertion sequences from Geobacillus stearothermophilus that encode several TnpB and IscBorthologues, and showed that a single TnpA transposase was broadlyactive for transposon mobilization. The donor joints formed upon religation of transposon-flanking sequences were efficiently targeted for cleavage by RNA-guided TnpB and IscB nucleases, and co-expression of TnpB and TnpA led to substantially greater transposon retention relative to conditions in which TnpA was expressed alone. Notably, TnpA and TnpB alsostimulated recombination frequencies, surpassing rates observed with TnpB alone. Collectively, this study reveals that RNA-guided DNA cleavage aroseas a primal biochemical activity to bias the selfish inheritance and spread of transposable elements, which was later co-opted during the evolution of CRISPR-Cas adaptive immunity for antiviral defence.

Prediction of demand for staple food and feed grain by a novel hybrid fractional discrete multivariate grey model

Increasing geopolitical conflicts, extreme weather and other emergencies are continuously affecting global agriculture and food systems, threatening national and regional food security. Therefore, it is particularly important to accurately predict national or regional grain demand. In this paper, a novel fractional discrete dynamic multivariate grey model is proposed to predict grain demand. Based on the discrete modeling idea, the model considers the impacts of the change trend of the related factor sequences, adds the linear correction term and the random disturbance term, and applies the fractional order accumulation strategy, which improves the accuracy and robustness. An algorithm based on sailfish optimizer is introduced to optimize the fractional order accumulation parameter of the model. Taking the Yangtze River Economic Belt as an example, the fitting and prediction results of the novel and the existing three models are compared. The novel model can better fit and predict the demand for staple and feed grain, which is superior compared to other models. The predictions show that demand for staple food and urban feed grain in the Yangtze River Economic Belt will increase to varying degrees, while rural feed grain demand will remain stable overall. This paper will help the government to better grasp the changes in the structure and quantity of staple food and feed grain demand in the Yangtze River Economic Belt and formulate efforts to ensure food security.

Redescription of Illiosentis cetratus Van Cleave, 1945 (Acanthocephala: Illiosentidae) from Menticirrhus undulatus (Girard) in California, with notes on Illiosentis furcatus from Peru.

Illiosentis Van Cleave et Lincicome, 1939 initially included two species: Illiosentis furcatus Van Cleave et Lincicome, 1939 found in the West Atlantic from Cape Cod in Massachusetts, USA to northern Argentina and Illiosentis cetratus Van Cleave, 1945 with restricted distribution in the Pacific coast of southern California. We are reporting I. furcatus from Peru for the first time and describe a population of I. cetratus from the California corbina, Menticirrhus undulatus (Girard), from southern California. The proboscis hook formula was 14 longitudinal rows for I. furcatus of 18-23 hooks each compared to 16 rows of 19-24 hooks each reported by Van Cleave (1945). We complete the inadequate description of I. cetratus with new information on sexual differentiation in the length of the trunk, dorsal vs. ventral hooks, hook roots, trunk spines, two types of anterior recurved rooted hooks vs. posterior rootless straight hooks, measurements of dorsal and ventral hooks and spines, shape of hook roots, terminal position of the female gonopore, and of position of the cephalic ganglion at the anterior margin of the trunk. We also include new details of the reproductive system in both sexes including Saefftigen's pouch and cement gland ducts. We present new SEM and light microscope images. The Energy Dispersive X-ray analysis (EDXA) shows a high level of sulfur in anterior, middle and posterior hooks in various hook sites, as well as spectra of hook tips with a higher relative concentration of sulfur compared to other hook sites. For the placement of I. cetratus, phylogenetic analysis of sequences of three molecular markers, 18S, 28S rRNA and mitochondrial cox 1 genes, was performed with other related available sequences. The resulting analysis illustrated that I. cetratus was nested within a separate clade along with species of two genera, Dentitruncus truttae Sinzar, 1955 and Neotegorhynchus cyprini Lisitsyna, Xi, Orosová, Barčák et Oros, 2022 represented our species of Illiosentis separate from species of Tegorhynchus Van Cleave, 1921 (as also according to the morphology) with which the Illiosentis species were previously synonymised.

Floral biology insights into essential oil yield and chemical composition in davana (Artemisia pallens Bess), a high-value aromatic plant of India

Floral organs are identified as the major source of essential oil production in some prime aromatic plants. The quality and quantity of the essential oil are also influenced by the floral developmental stages. The present study was undertaken in A. pallens Bess (davana) with respect to its floral biology and floral sequence in relation to the essential oil yield and its chemical constituents for industrial extraction. The findings revealed that floral (inflorescence) biomass is the primary source of essential oil yield in davana, with the highest oil yield (0.90 ml/100 g) recovered during the blooming stage, followed by herbage (stems and leaves) biomass. Furthermore, cis-davanone, the major chemical constituent of davana essential oil, was recorded at a higher percentage in the bud stage (66.36±0.60%) followed by the blooming stage (60.56±0.20%) and the seed setting stage (40.54±0.80%). These findings can be used to optimize harvest timing in order to obtain higher quality and quantity of davana essential oil.

The microbial biodiversity at the archeological site of Tel Megiddo (Israel).

The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes. We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically. We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former. We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.

Degradation of starch-based bioplastic bags in the pelagic and benthic zones of the Gulf of Oman

The Gulf of Oman is becoming increasingly polluted with plastics, hence bioplastics have been considered ‘a substitute’, although their biodegradability in marine environments has not been well investigated. Most research has been performed on cellulose-based bioplastics, whereas starch-based bioplastics have proven to be a suitable, but less researched, alternative. This study is the first of its kind designed to investigate the degradability of two different types of starch-based bioplastic bags, available in the market and labeled as “biodegradable”, in the pelagic and benthic zones of one of the warmest marine environment in the world. Fourier-Transform Infrared Spectroscopy (FTIR) showed a clear reduction in the presence of OH, CH, and CO in the bioplastic bags after 5 weeks of immersion. Thermo-Gravimetric Analysis (TGA) indicated degradation of glycerol, starch, and polyethylene. The biofouling bacterial communities on bioplastic surfaces showed distinct grouping based on the immersion zone. Candidaatus saccharibacteria, Verrucomicrobiae, Acidimicrobiia and Planctomycetia sequences were only detectable on bioplastics in the pelagic zone, whereas Actinomyces, Pseudomonas, Sphingobium and Acinetobacter related sequences were only found on bioplastics in the benthic layer. We conclude that starch-based bioplastics are more readily degradable in the Gulf of Oman than conventional plastics, hence could serve as a better environmentally friendly alternative.

First report of L1 cell adhesion molecule (L1CAM) in flat fish (Starry flounder): Molecular features and expression analysis

In this study, the starry flounder L1 cell adhesion molecule (L1CAM) sequence was obtained using next-generation sequencing, and the integrity of the sequence was verified by cloning and sequencing. First, the amino acid sequence was predicted using the cDNA sequence, and the gene was then identified through multiple sequence alignment analysis with related sequences and phylogenetic analysis. Thus, homogeneity was confirmed. The expression level of PsL1CAM (Platichthys stellatus L1CAM) mRNA in healthy starry flounder was detected in all tissues used in the experiment, and tissue- and gene-specific expression levels were confirmed. In addition, as a result of mRNA expression analysis after artificial infection with viral hemorrhagic septicemia virus (VHSV) and Streptococcus parauberis PH0710, significant expression changes and characteristics were confirmed following infection with VHSV and S. parauberis PH0710. After artificial infection with VHSV, the expression level of PsL1CAM mRNA was significantly upregulated in almost all major tissues of the starry flounder, whereas it was significantly downregulated in mucosal-associated lymphoid tissues, such as the gills and intestine. Infection with S. parauberis PH0710 significantly upregulated the expression of PsL1CAM mRNA in almost all major tissues of the starry flounder, whereas it was significantly downregulated in the heart after infection. Our results indicate that PsL1CAM may be involved in the host immune response to starry flounders.