A comparative analysis of phage classification methods in light of the recent ICTV taxonomic revisions

Recent ICTV taxonomy updates significantly changed phage taxonomy, yet a thorough phage classification workflow doesn't exist. This study compares six categorization tools and establishes a novel multi-method approach, combining genome similarity and specialized protein analysis. Applying the method to APEC phage P151 showed consistent categorization across platforms. A possible workflow for phage classification is proposed; offering a versatile tool for phage research and development.

[18F]AlF-NOTA-PCP2: a novel PET/CT tracer for enhanced PD-L1 heterogeneity imaging and comparative analysis with [18F]AlF-NOTA-WL12 in glioblastoma xenografts

PURPOSE

The unsatisfactory efficacy of PD-L1 antibodies in glioblastoma (GBM) is largely due to the temporal and spatial heterogeneity of PD-L1 expression. Molecular imaging can enhance understanding of the tumor immune microenvironment and guide immunotherapy. However, highly sensitive imaging agents capable of effectively visualizing PD-L1 heterogeneity are limited. This study introduces a novel PET tracer, offering improved imaging of PD-L1 heterogeneity in GBM xenografts, with a comparative analysis to [18F]AlF-NOTA-WL12.

METHODS

[18F]AlF-NOTA-PCP2 was synthesized with high purity and its affinity for PD-L1 was characterized using surface plasmon resonance (SPR) and cell binding assays. Its specificity for PD-L1 was evaluated both in vitro using various cell lines and in vivo with GBM xenograft models in NOD/SCID mice. PET/CT imaging was conducted to evaluate the tracer's biodistribution, pharmacokinetics, and ability to quantify tumoral spatial heterogeneity of PD-L1 expression. A focused comparative analysis between [18F]AlF-NOTA-PCP2 and [18F]AlF-NOTA-WL12 was conducted, examining binding affinity, biodistribution, pharmacokinetics, and imaging effectiveness in GBM xenografts. Additionally, human radiation dosimetry estimates compared the safety profiles of both tracers.

RESULTS

[18F]AlF-NOTA-PCP2 demonstrated high radiochemical purity (> 95%) and a strong affinity for PD-L1, comparable to [18F]AlF-NOTA-WL12. In vitro and in vivo studies confirmed its specificity for PD-L1, with increased uptake in PD-L1 expressing cells and tumors. Toxicological profiles indicated no significant abnormalities in serum biochemical indicators or major organ tissues. MicroPET/CT imaging showed [18F]AlF-NOTA-PCP2's effectiveness in visualizing PD-L1 expression levels and spatial heterogeneity in GBM xenografts. Comparative studies revealed [18F]AlF-NOTA-PCP2's improved pharmacokinetic properties, including higher tumor-to-blood ratios and lower nonspecific liver uptake, as well as reduced radiation exposure compared to [18F]AlF-NOTA-WL12.

CONCLUSION

[18F]AlF-NOTA-PCP2 distinguishes itself as an exceptionally sensitive PET/CT tracer, adept at non-invasively and accurately quantifying PD-L1 expression and its spatial heterogeneity in tumors, especially in GBM. Its favorable pharmacokinetic properties, safety profile, and high affinity for PD-L1 highlight its potential for enhancing the precision of cancer immunotherapy and guiding individualized treatment strategies. While promising, its clinical translation, especially in brain imaging, necessitates further validation in clinical trials.

Civil service organization as a political determinant of health: Analyzing relationships between merit-based hiring, corruption, and population health

A growing literature finds that the way governments are organized can impact the societies they serve in important ways. The same is apparent with respect to civil service organizations. Numerous studies show that the recruitment of civil servants based on their credentials rather than on nepotism or patronage reduces corruption in government. Political corruption in turn appears to harm population health. Up to this time, however, civil service organization is not a recognized determinant of health and is little discussed outside of political science disciplines. To provoke a broader conversation on this subject, the following study proposes that meritocratic recruitment of civil servants improves population health. To test this proposition, a series of regression models examines comparative data for 118 countries. Consistent with study hypotheses, meritocratic recruitment of civil servants corresponds longitudinally with both lower rates of corruption and lower rates of infant mortality. Results are similar after robustness checks. Findings with regard to life expectancy are more mixed. However, additional tests suggest meritocratic recruitment contributes to life expectancy over a longer span of time. Findings also offer more support for a direct pathway from meritocratic recruitment to population health rather than via changes in corruption levels per se, although this may depend on a country's level of economic development. Overall, this study offers first evidence that civil service organization, particularly the recruitment of civil servants based on the merits of their applications rather than on whom they happen to know in government, is a positive determinant of health. More research in this area is needed.

Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships

BACKGROUND

Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time.

RESULTS

The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections.

CONCLUSIONS

This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.

Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

BACKGROUND

Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species.

RESULTS

In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum.

CONCLUSION

Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.

Comparative analysis of chloroplast genomes of Pulsatilla species reveals evolutionary and taxonomic status of newly discovered endangered species Pulsatilla saxatilis

BACKGROUND

Pulsatilla saxatilis, a new species of the genus Pulsatilla has been discovered. The morphological information of this species has been well described, but its chloroplast genome characteristics and comparison with species of the same genus remain to be reported.

RESULTS

Our results showed that the total length of chloroplast (cp.) genome of P. saxatilis is 162,659 bp, with a GC content of 37.5%. The cp. genome contains 134 genes, including 90 known protein-coding genes, 36 tRNA genes, and 8 rRNA genes. P. saxatilis demonstrated similar characteristics to other species of genus Pulsatilla. Herein, we compared cp. genomes of 10 species, including P. saxatilis, and found that the cp. genomes of the genus Pulsatilla are extremely similar, with a length of 162,322-163,851 bp. Furthermore, The SSRs of Pulsatilla ranged from 10 to 22 bp in length. Among the four structural regions of the cp. genome, most long repeats and SSRs were detected in the LSC region, followed by that in the SSC region, and least in IRA/ IRB regions. The most common types of long repeats were forward and palindromic repeats, followed by reverse repeats, and only a few complementary repeats were found in 10 cp. genomes. We also analyzed nucleotide diversity and identified ccsA_ndhD, rps16_trnK-UUU, ccsA, and rbcL, which could be used as potential molecular markers for identification of Pulsatilla species. The results of the phylogenetic tree constructed by connecting the sequences of high variation regions were consistent with those of the cp. gene phylogenetic tree, and the species more closely related to P. saxatilis was identified as the P. campanella.

CONCLUSION

It was determined that the closest species to P. saxatilis is P. campanella, which is the same as the conclusion based on pollen grain characteristics, but different from the P. chinensis determined based on morphological characteristics. By revealing information on the chloroplast characteristics, development, and evolution of the cp. genome and the potential molecular markers, this study provides effective molecular data regarding the evolution, genetic diversity, and species identification of the genus Pulsatilla.

Comparative genomics on chloroplasts of Rubus (Rosaceae)

Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.

Innovative food-upcycling solutions: Comparative analysis of edible films from kimchi-extracted cellulose, sorbitol, and citric acid for food packaging applications

In this study, kimchi-extracted cellulose was utilized to fabricate edible films using a hot synthetic approach, followed by solvent casting, and employing sorbitol and citric acid as the plasticizer and crosslinker, respectively. The chemical, optical, physical, and thermal properties of these films were explored to provide a comparative assessment of their suitability for various packaging applications. Chemical analyses confirmed that the kimchi-extracted cellulose comprised cellulose Iβ and amorphous cellulose and did not contain any impurities. Optical analyses revealed that kimchi-extracted cellulose-containing films exhibited better-dispersed surfaces than films fabricated from commercial cellulose. Physical property analyses indicated their hydrophilic characteristics with contact angles <20°. In the thermal analysis, similar Tg results confirmed the comparable thermal stability between films containing commercial microcrystalline cellulose-containing films and kimchi-extracted cellulose-containing films. Edible films produced from kimchi-extracted cellulose through food-upcycling approaches are therefore promising for applications as packaging materials.

Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value

BACKGROUND

Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published.

RESULTS

Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647 bp in length and consisted of 19 circular subgenomes ranging in size from 21,995 bp to 48,212 bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes.

CONCLUSION

In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.

Evaluating plans for sustainable development in Arctic cities

Cities located in the Arctic often have extreme geographic and environmental contexts and unique sociopolitical and economic trajectories that, when combined with amplified effects of climate change in the region, impact future sustainable development. Well-recognized and standardized sustainable development indicator (SDI) frameworks such as ISO 37120 or UN-Habitat City Prosperity Index are often used to compare data across cities globally using comprehensive sets of indicators. While such indexes help characterize progress toward development and guide short- and long-term decision-making, they often lack relevance to specific contexts or characterize future visions of urban growth. To evaluate the extent of these deficiencies and to provide a comparative analysis of approaches to sustainable urban growth in the Arctic, this paper analyzes city planning documents for five northern cities - Anchorage (USA), Utqiagvik (USA), Reyjavik (ISL), Iqaluit, (CAN), Whitehorse, (CAN) - for goals, targets, and indicators and compare these to thematic areas and indicators defined by ISO 37120:2018 Sustainable Cities and Communities. The results confirm that although international SDI frameworks may be useful for comparative analysis of cities across diverse regions, they exclude important local factors that influence goal-oriented urban sustainability planning strategies employed in the Arctic region.

Plastid genomes provide insights into the phylogeny and chloroplast evolution of the paper daisy tribe Gnaphalieae (Asteraceae)

Chloroplast genomes, as an essential source of phylogenetic information, are increasingly utilized in the evolutionary study of angiosperms. Gnaphalieae is a medium-sized tribe of the sunflower family of Asteraceae, with about 2,100 species in 178 genera distributed in temperate habitats worldwide. There has been considerable progress in our understanding of their phylogenetic evolution using both nuclear and chloroplast sequences, but no focus on chloroplast genomic data. In this study, we performed sequencing, assembly, and annotation of 16 representative chloroplast genomes from all the major lineages of Gnaphalieae. Our results showed that the plastomes exhibited a typical circular tetrad structure with similar genomic structure gene content. But there were differences in genome size, SSRs, and codon usage within the tribe. Phylogenetic analysis revealed Relhania clade is the earliest diverged lineages with the Lasiopogon clade and the Gnaphalium s.s. clade diverged subsequently. The core group includes FLAG clade sister to the HAP and Australasian group. Compared with the outgroup species, chloroplast genome size of the FLAG clade is much reduced whereas those of Australasian, HAP, Gnaphalium s.s., Lasiopogon and Relhania clades are relatively expanded. Insertions and deletions in the intergenic regions associated with repetitive sequence variations are supposed to be the main factor leading to length variations in the chloroplast genomes of Gnaphalieae. The comparative analyses of chloroplast genomes would provide useful implications into understanding the taxonomic and evolutionary history of Gnaphalieae.

Melanoidin-like carbohydrate-containing macromolecules from Shanxi aged vinegar exert immunoenhancing effects on macrophage RAW264.7 cells

Bioactive macromolecule mining is important for the functional chemome analysis of traditional Chinese vinegar. In this study, we isolated and characterized carbohydrate-containing macromolecules from Shanxi aged vinegar (CCMSAV) and evaluated their immunomodulatory activity. The isolation process involved ethanol precipitation, deproteinization, decolorization, and DEAE-650 M column chromatography, resulting in the acquisition of four sub-fractions. All sub-fractions exhibited a molecular weight range of 6.92 to 16.71 kDa and were composed of 10 types of monosaccharides. Comparative analysis of these sub-fractions with two melanoidins exhibited similarities in elemental composition, spectral signature, and pyrolytic characteristics. Immunological assays confirmed the significantly enhanced cell viability, phagocytic activity, and secretion of nitric oxide, tumor necrosis factor (TNF)-α and interleukin (IL)-6 in RAW264.7 cells by all four sub-fractions. Further investigation of the immunomodulatory mechanism revealed that SAV-RP70-X, the most potent purified sub-fraction, enhanced aerobic glycolysis in macrophages and activated Toll-like receptor 2 (TLR2), TLR4, mannose receptor (MR), scavenger receptor (SR), and the dendritic cell-associated C-type lectin-1 receptor (Dectin-1). Furthermore, the activation of macrophages was associated with the MyD88/PI3K/Akt/NF-κB signaling pathway. Methylation analysis revealed that 1,4-Xylp was the most abundant glycosidic linkage in SAV-RP70-X.

Basic Statistics, Statistical Design, and Critical Analysis of Statistics for Surgeons

Statistics is a set of tools used in medical decision-making no different than how a scalpel or a sagittal saw is used in the operating room. No foot and ankle surgeon is born with the inherent ability to perform, understand, and critically interpret them. Instead, it requires training and practice throughout the course of a career in medicine to develop a working proficiency. This article reviews the basic indications and interpretation of common descriptive and comparative statistical tests in the podiatric literature. Additionally, the concept of which tests are most appropriate for which investigational methodologies is introduced.

Comparative analysis and prediction of avian influenza in Shangrao city, China from 2016 to 2022

The aim of this study was to investigate the effects of vaccination, COVID-19 pandemic and migration of migratory birds on the avian influenza positivity rate in Shangrao City and to predict the future avian influenza positivity rate. Real-time reverse transcription polymerase chain reaction (RT-PCR) was used to detect nucleic acids of avian influenza A viruses. 1795 samples were collected between 2016 and 2022, of which 1086 were positive. In addition, there were seven human cases of avian influenza. The results showed that the positivity rate of H9 subtype in Shangrao City was higher than usual during the COVID-19 pandemic and migratory birds. Predictions suggest that the H9 subtype positivity rate in Shangrao City will be on the rise in the future. In recent years, the H5 positivity rate has gradually increased. Migratory birds and the COVID-19 pandemic have led to an increase in H9 subtype positivity. Therefore, the prevention and control of them should be strengthened.

Is convenience really king? Comparative evaluation of catastrophic costs due to tuberculosis in the public and private healthcare sectors of Viet Nam: a longitudinal patient cost study

BACKGROUND

In Viet Nam, tuberculosis (TB) represents a devastating life-event with an exorbitant price tag, partly due to lost income from daily directly observed therapy in public sector care. Thus, persons with TB may seek care in the private sector for its flexibility, convenience, and privacy. Our study aimed to measure income changes, costs and catastrophic cost incurrence among TB-affected households in the public and private sector.

METHODS

Between October 2020 and March 2022, we conducted 110 longitudinal patient cost interviews, among 50 patients privately treated for TB and 60 TB patients treated by the National TB Program (NTP) in Ha Noi, Hai Phong and Ho Chi Minh City, Viet Nam. Using a local adaptation of the WHO TB patient cost survey tool, participants were interviewed during the intensive phase, continuation phase and post-treatment. We compared income levels, direct and indirect treatment costs, catastrophic costs using Wilcoxon rank-sum and chi-squared tests and associated risk factors between the two cohorts using multivariate regression.

RESULTS

The pre-treatment median monthly household income was significantly higher in the private sector versus NTP cohort (USD 868 vs USD 578; P = 0.010). However, private sector treatment was also significantly costlier (USD 2075 vs USD 1313; P = 0.005), driven by direct medical costs which were 4.6 times higher than costs reported by NTP participants (USD 754 vs USD 164; P < 0.001). This resulted in no significant difference in catastrophic costs between the two cohorts (Private: 55% vs NTP: 52%; P = 0.675). Factors associated with catastrophic cost included being a single-person household [adjusted odds ratio (aOR = 13.71; 95% confidence interval (CI): 1.36-138.14; P = 0.026], unemployment during treatment (aOR = 10.86; 95% CI: 2.64-44.60; P < 0.001) and experiencing TB-related stigma (aOR = 37.90; 95% CI: 1.72-831.73; P = 0.021).

CONCLUSIONS

Persons with TB in Viet Nam face similarly high risk of catastrophic costs whether treated in the public or private sector. Patient costs could be reduced through expanded insurance reimbursement to minimize direct medical costs in the private sector, use of remote monitoring and multi-week/month dosing strategies to avert economic costs in the public sector and greater access to social protection mechanism in general.

Supporting patient decision-making in non-invasive prenatal testing: a comparative study of professional values and practices in England and France

BACKGROUND

Non-invasive prenatal testing (NIPT), which can screen for aneuploidies such as trisomy 21, is being implemented in several public healthcare systems across Europe. Comprehensive communication and information have been highlighted in the literature as important elements in supporting women's reproductive decision-making and addressing relevant ethical concerns such as routinisation. Countries such as England and France are adopting broadly similar implementation models, offering NIPT for pregnancies with high aneuploidy probability. However, we do not have a deeper understanding of how professionals' counselling values and practices may differ between these contexts.

METHODS

In this paper, we explore how professionals in England and France support patient decision-making in the provision of NIPT and critically compare professional practices and values. We draw on data from semi-structured interviews with healthcare professionals.

RESULTS

Both English and French professionals emphasised values relating to patient choice and consent. However, understandings and application of these values into the practice of NIPT provision differed. English interviewees placed a stronger emphasis on interpreting and describing the process of counselling patients and clinical care through a "principle" lens. Their focus was on non-directiveness, standardisation, and the healthcare professional as "decision-facilitator" for patients. French interviewees described their approach through a "procedural" lens. Their focus was on formal consent, information, and the healthcare professional as "information-giver". Both English and French professionals indicated that insufficient resources were a key barrier in effectively translating their values into practice.

CONCLUSION

Our findings illustrate that supporting patient choice in the provision of NIPT may be held as an important value in common on a surface level, but can be understood and translated into practice in different ways. Our findings can guide further research and beneficially inform practice and policy around NIPT provision.

In-Silico Identification, Characterization and Expression Analysis of Genes Involved in Resistant Starch Biosynthesis in Potato (Solanum tuberosum L.) Varieties

Potato (Solanum tuberosum L.), an important horticultural crop is a member of the family Solanaceae and is mainly grown for consumption at global level. Starch, the principal component of tubers, is one of the significant elements for food and non-food-based applications. The genes associated with biosynthesis of starch have been investigated extensively over the last few decades. However, a complete regulation pathway of constituent of amylose and amylopectin are still not deeply explored. The current in-silico study of genes related to amylose and amylopectin synthesis and their genomic organization in potato is still lacking. In the current study, the nucleotide and amino acid arrangement in genome and twenty-two genes linked to starch biosynthesis pathway in potato were analysed. The genomic structure analysis was also performed to find out the structural pattern and phylogenetic relationship of genes. The genome mining and structure analysis identified ten specific motifs and phylogenetic analysis of starch biosynthesis genes divided them into three different clades on the basis of their functioning and phylogeny. Quantitative real-time PCR (qRT-PCR) of amylose biosynthesis pathway genes in three contrast genotypes revealed the down-gene expression that leads to identify potential cultivar for functional genomic approaches. These potential lines may help to achieve higher content of resistant starch.

Comparative study of the quality indices, antioxidant substances, and mineral elements in different forms of cabbage

BACKGROUND

As the second largest leafy vegetable, cabbage (Brassica oleracea L. var. capitata) is grown globally, and the characteristics of the different varieties, forms, and colors of cabbage may differ. In this study, five analysis methods-variance analysis, correlation analysis, cluster analysis, principal component analysis, and comprehensive ranking-were used to evaluate the quality indices (soluble protein, soluble sugar, and nitrate), antioxidant content (vitamin C, polyphenols, and flavonoids), and mineral (K, Ca, Mg, Cu, Fe, Mn, and Zn) content of 159 varieties of four forms (green spherical, green oblate, purple spherical, and green cow heart) of cabbage.

RESULTS

The results showed that there are significant differences among different forms and varieties of cabbage. Compared to the other three forms, the purple spherical cabbage had the highest flavonoid, K, Mg, Cu, Mn, and Zn content. A scatter plot of the principal component analysis showed that the purple spherical and green cow heart cabbage varieties were distributed to the same quadrant, indicating that their quality indices and mineral contents were highly consistent, while those of the green spherical and oblate varieties were irregularly distributed. Overall, the green spherical cabbage ranked first, followed by the green cow heart, green oblate, and purple spherical varieties.

CONCLUSIONS

Our results provide a theoretical basis for the cultivation and high-quality breeding of cabbage.

Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae)

BACKGROUND

Ampelopsideae J. Wen & Z.L. Nie is a small-sized tribe of Vitaceae Juss., including ca. 47 species from four genera showing a disjunct distribution worldwide across all the continents except Antarctica. There are numerous species from the tribe that are commonly used as medicinal plants with immune-modulating, antimicrobial, and anti-hypertensive properties. The tribe is usually recognized into three clades, i.e., Ampelopsis Michx., Nekemias Raf., and the Southern Hemisphere clade. However, the relationships of the three clades differ greatly between the nuclear and the plastid topologies. There has been limited exploration of the chloroplast phylogenetic relationships within Ampelopsideae, and studies on the chloroplast genome structure of this tribe are only available for a few individuals. In this study, we aimed to investigate the evolutionary characteristics of plastid genomes of the tribe, including their genome structure and evolutionary insights.

RESULTS

We sequenced, assembled, and annotated plastid genomes of 36 species from the tribe and related taxa in the family. Three main clades were recognized within Ampelopsideae, corresponding to Ampelopsis, Nekemias, and the Southern Hemisphere lineage, respectively, and all with 100% bootstrap supports. The genome sequences and content of the tribe are highly conserved. However, comparative analyses suggested that the plastomes of Nekemias demonstrate a contraction in the large single copy region and an expansion in the inverted repeat region, and possess a high number of forward and palindromic repeat sequences distinct from both Ampelopsis and the Southern Hemisphere taxa.

CONCLUSIONS

Our results highlighted plastome variations in genome length, expansion or contraction of the inverted repeat region, codon usage bias, and repeat sequences, are corresponding to the three lineages of the tribe, which probably faced with different environmental selection pressures and evolutionary history. This study provides valuable insights into understanding the evolutionary patterns of plastid genomes within the Ampelopsideae of Vitaceae.

The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis

BACKGROUND

Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus.

RESULTS

In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis.

CONCLUSIONS

Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.

Comparative Analysis of Parasite Load on Recently Established Invasive Pumpkinseed Lepomis gibbosus (Actinopterygii: Centrarchidae) in Europe

PURPOSE

The aim of this study was the comparative analysis of the parasite communities of new populations of invasive pumpkinseed (Lepomis gibbosus) in western Ukraine with pumpkinseed from Czechia, where populations have rapidly expanded over the last two decades.

METHODS

Sampling took place at three localities in the western part of Ukraine (i.e. Dobrotvir Reservoir (Vistula basin), Burshtyn Reservoir (Dniester basin), Mynai Pond (Danube basin)) and four in Czechia (i.e. Oxbow D2, Heršpický Pond (Danube basin), and Kolín oxbow and Římov Reservoir (Elbe basin).

RESULTS

In total, 11 parasite taxa were recorded in Ukraine and 17 in Czechia. Four species were co-introduced from North America with their host, i.e. the myxosporean Myxobolus dechtiari, the monogeneans Onchocleidus dispar and Onchocleidus similis, and metacercariae of a trematode Posthodiplostomum centrarchi. High dominance indices were related to a high abundance of co-introduced parasites, i.e. O. similis in Mynai pond and P. centrarchi in Dobrotvir Reservoir. Overall abundance of acquired parasites was generally low.

CONCLUSION

This study shows that parasite communities in recently established pumpkinseed populations in the western part of Ukraine and Czechia are less diverse than those established in Europe for decades. The generally low parasite load in these new populations may play an important role in their ability to successfully establish and create strong populations by providing a competitive advantage over local species.

Cancer care pathways across seven countries in Europe: What are the current obstacles? And how can artificial intelligence help?

BACKGROUND

Cancer poses significant challenges for healthcare professionals across the disease pathway including cancer imaging. This study constitutes part of the user requirement definition of INCISIVE EU project. The project has been designed to explore the full potential of artificial intelligence (AI)-based technologies in cancer imaging to streamline diagnosis and management. The study aimed to map cancer care pathways (breast, prostate, colorectal and lung cancers) across INCISIVE partner countries, and identify bottle necks within these pathways.

METHODS

Email interviews were conducted with ten oncology specialised healthcare professionals representing INCISIVE partner countries: Greece, Cyprus, Spain, Italy, Finland, the United Kingdom (UK) and Serbia. A purposive sampling strategy was employed for recruitment and data was collected between December 2020 and April 2021. Data was entered into Microsoft Excel spreadsheet to allow content examination and comparative analysis.

RESULTS

The analysed pathways all shared a common characteristic: inequalities in relation to delays in cancer diagnosis and treatment. All the studied countries, except the UK, lacked official national data about diagnostic and therapeutic delays. Furthermore, a considerable variation was noted regarding the availability of imaging and diagnostic services across the seven countries. Several concerns were also noted for inefficiencies/inequalities with regards to national screening for the four investigated cancer types.

CONCLUSIONS

Delays in cancer diagnosis and treatment are an ongoing challenge and a source for inequalities. It is important to have systematic reporting of diagnostic and therapeutic delays in all countries to allow the proper estimation of its magnitude and support needed to address it. Our findings also support the orientation of the current policies towards early detection and wide scale adoption and implementation of cancer screening, through research, innovation, and technology. Technologies involving AI can have a great potential to revolutionise cancer care delivery.

POLICY SUMMARY

This study highlights the widespread delay in cancer diagnosis across Europe and supports the need for, systematic reporting of delays, improved availability of imaging services, and optimised national screening programs. The goal is to enhance cancer care delivery, encourage early detection, and implement research, innovation, and AI-based technologies for improved cancer imaging.

Which model is more efficient in carbon emission prediction research? A comparative study of deep learning models, machine learning models, and econometric models

Accurately predicting future carbon emissions is of great significance for the government to scientifically promote carbon emission reduction policies. Among the current technologies for forecasting carbon emissions, the most prominent ones are econometric models and deep learning, but few works have systematically compared and analyzed the forecasting performance of the methods. Therefore, the paper makes a comparison for deep learning model, machine learning model, and the econometric model to demonstrate whether deep learning is an efficient method for carbon emission prediction research. In model mechanism, neural network for deep learning refers to an information processing model established by simulating biological neural system, and the model can be further extended through bionic characteristics. So the paper further optimizes the model from the perspective of bionics and proposes an innovative deep learning model based on the memory behavior mechanism of group creatures. Comparison results show that the prediction accuracy of the heuristic neural network is higher than that of the econometric model. Through in-depth analysis, the heuristic neural network is more suitable for predicting future carbon emissions, while the econometric model is more suitable for clarifying the impact of influencing factors on carbon emissions.

Complications and clinical outcomes with minimally invasive plate osteosynthesis (MIPO) technique for midshaft clavicle fractures: a systematic review and meta-analysis

Background

Clavicle fractures are among the most common upper limb fractures in adults, with the midshaft region being the most frequently affected site. Minimally invasive plate osteosynthesis (MIPO) has emerged as an alternative to the traditional open reduction and internal fixation (ORIF) technique, offering potential advantages. The purpose of this study was to conduct a systematic review to explore the results of this technique in the existing literature, with emphasis on the occurrence of surgical complications and functional outcomes and also to provide a comprehensive comparison of MIPO and ORIF in the management of midshaft clavicle fractures.

Methods

We conducted a systematic review to evaluate the complication incidence and clinical outcomes of MIPO for midshaft clavicle fractures. We searched PubMed/Medical Literature Analysis and Retrieval System Online (MEDLINE), Scopus, the Cochrane Database of Controlled Trials, and the Cochrane Database of Systematic Reviews databases without language or date restrictions. Studies focusing on midshaft clavicle fractures treated with MIPO were included, while other clavicle fractures and nonclinical studies were excluded. The risk of bias was assessed using the Methodological Index for Nonrandomized Studies criteria and the Risk of Bias Tool 2 Cochrane tool. Data synthesis included qualitative analysis, and if applicable, quantitative analysis and meta-analysis. Adherence to Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines ensured reporting quality.

Results

A total of 107 studies were initially identified, after applying inclusion and exclusion criteria, 22 studies were included for data extraction. These studies involved the evaluation of 714 clavicles treated with the MIPO technique. Of the 714 MIPO cases, 11 cases of implant failure, 5 nonunions, 2 infections, and 28 cases with neurological impairment were observed. Quantitative analysis comparing MIPO with ORIF revealed that MIPO had significantly shorter surgery time (mean difference -12.95, 95% confidence interval [-25.27 to -0.63], P = .04) and lower occurrence of numbness (odds ratio 0.29, 95% CI [0.15-0.56], P = .0002) compared to ORIF. Time to bone union, functional outcomes, and other complications were similar between MIPO and ORIF at the final follow-up. An overall moderate risk of bias was found across the studies.

Conclusion

The MIPO technique yields good and comparable results to ORIF for midshaft clavicle fractures. Additionally, the MIPO technique may offer advantages such as reduced surgical time and lower chances of neurological impairment.

Uncovering nutrients and energy related gene functions of black soldier fly Hermetia illucens strain KUP

The black soldier fly (Hermetia illucens) has emerged as a significant insect species in the decomposition of organic waste for sustainable agricultural practices. Due to its remarkable characteristics and performance, H. illucens is increasingly utilised for insect farming, particularly for industrial-scale rearing throughout the world. In this study, we employed whole-genome sequencing to annotate the gene and protein functions of H. illucens and to explore the functional genomics related to nutrients and energy. As a result, a genome size of H. illucens strain KUP 1.68 Gb with a GC content of 42.13 % was achieved. Of the 14,036 coding sequences, we determined the function of 12,046 protein-coding genes. Based on metabolic functional assignment, we classified 4,218 protein-coding genes; the main category was metabolism (32.86 %). Comparative genomic analysis across the other H. illucens strain and insect species revealed that the major metabolic gene functions and pathways related to nutrient and energy sources of H. illucens KUP are involved in key amino acid metabolism (e.g., cysteine and methionine) as well as fatty acid biosynthesis and glycerolipid metabolism. These findings underscore the metabolic capability and versatility of H. illucens, which is regarded as a potential source of proteins and lipids. Our study contributes to the knowledge regarding the feed utilisation of H. illucens and offers insights into transforming waste into valuable products. H. illucens has the potential to create globally sustainable nutrients and environmentally friendly solutions, aligning with the goal of responsible resource utilisation.

scEM: A New Ensemble Framework for Predicting Cell Type Composition Based on scRNA-Seq Data

With the advent of single-cell RNA sequencing (scRNA-seq) technology, many scRNA-seq data have become available, providing an unprecedented opportunity to explore cellular composition and heterogeneity. Recently, many computational algorithms for predicting cell type composition have been developed, and these methods are typically evaluated on different datasets and performance metrics using diverse techniques. Consequently, the lack of comprehensive and standardized comparative analysis makes it difficult to gain a clear understanding of the strengths and weaknesses of these methods. To address this gap, we reviewed 20 cutting-edge unsupervised cell type identification methods and evaluated these methods comprehensively using 24 real scRNA-seq datasets of varying scales. In addition, we proposed a new ensemble cell-type identification method, named scEM, which learns the consensus similarity matrix by applying the entropy weight method to the four representative methods are selected. The Louvain algorithm is adopted to obtain the final classification of individual cells based on the consensus matrix. Extensive evaluation and comparison with 11 other similarity-based methods under real scRNA-seq datasets demonstrate that the newly developed ensemble algorithm scEM is effective in predicting cellular type composition.

A comparative national-level analysis of government food system resilience activities across four developed countries at varying stages of planning

BACKGROUND

The COVID-19 pandemic, extreme weather events, and the Russian invasion of Ukraine have highlighted global food system vulnerabilities and a lack of preparedness and prospective planning for increasingly complex disruptions. This has spurred an interest in food system resilience. Despite the elevated interest in food system resilience, there is a lack of comparative analyses of national-level food system resilience efforts. An improved understanding of the food system resilience landscape can support and inform future policies, programs, and planning.

METHODS

We conducted a cross-country comparison of national-level food system resilience activities from Australia, Aotearoa New Zealand, Sweden, and the United States. We developed upon and adapted the resilience framework proposed by Harris and Spiegel to compare actions derived from thirteen national food system resilience documents. We coded the documents based on the actions taken by the governments including: the food system resilience attributes utilized, the part of the food supply chain, the specific shocks or stressors, the implementation level, the temporal focus of action, and the expected impact on food security. We analyzed and compared countries' coded categories and subcategories, and category combinations.

RESULTS

The results showed that these countries are addressing some of the same issues, are using multi-pronged policy actions to address food system resilience issues, and are focused on both retrospective reviews and prospective models of disruptive events to inform their decisions. Some work has been done towards preparing for climate change and other natural disasters, and less preparing has been done for other shocks or stressors.

CONCLUSIONS

This paper develops and applies a framework rooted in literature to understand the content of national-level food system resilience documents. The analysis identified potential gaps, concentrations, and themes in national food systems resilience. The framework can be applied to augment existing policy, create new policy, as well as to supplement and complement other existing frameworks.

Clinical utility of handheld fundus and smartphone-based camera for monitoring diabetic retinal diseases: a review study

Diabetic retinopathy (DR) is the leading global cause of vision loss, accounting for 4.8% of global blindness cases as estimated by the World Health Organization (WHO). Fundus photography is crucial in ophthalmology as a diagnostic tool for capturing retinal images. However, resource and infrastructure constraints limit access to traditional tabletop fundus cameras in developing countries. Additionally, these conventional cameras are expensive, bulky, and not easily transportable. In contrast, the newer generation of handheld and smartphone-based fundus cameras offers portability, user-friendliness, and affordability. Despite their potential, there is a lack of comprehensive review studies examining the clinical utilities of these handheld (e.g. Zeiss Visuscout 100, Volk Pictor Plus, Volk Pictor Prestige, Remidio NMFOP, FC161) and smartphone-based (e.g. D-EYE, iExaminer, Peek Retina, Volk iNview, Volk Vistaview, oDocs visoScope, oDocs Nun, oDocs Nun IR) fundus cameras. This review study aims to evaluate the feasibility and practicality of these available handheld and smartphone-based cameras in medical settings, emphasizing their advantages over traditional tabletop fundus cameras. By highlighting various clinical settings and use scenarios, this review aims to fill this gap by evaluating the efficiency, feasibility, cost-effectiveness, and remote capabilities of handheld and smartphone fundus cameras, ultimately enhancing the accessibility of ophthalmic services.

Comparative analysis of microbial succession and proteolysis focusing on amino acid pathways in Asiago-PDO cheese from two dairies

In this study, a comprehensive and comparative analysis was conducted on Italian Asiago-PDO cheese obtained from two different dairies named Dairy I and Dairy II using industrial and natural fermented milk, respectively. The analysis encompassed the evaluation of chemical composition, the succession of the microbiota during manufacture and ripening, and proteolysis mainly focusing on free individual amino acid (FAA) profiles. A metagenomic approach was used to investigate the cheese microbiome functionality. Differences in gross chemical composition were more evident during ripening, with Dairy II showing higher variability within batches. The microbiota varied significantly between the two dairies and ripening stages. The choice of starter culture shaped the microbiota during production and affected the microbial diversity of non-starter lactic acid bacteria (NSLAB) originated from the raw milk during ripening. Peptide chromatographic profiles and FAA concentrations increased as ripening progressed, with Dairy I showing higher production of FAA. Functional analysis of the metagenomes linked species to specific amino acid metabolism/catabolism pathways. The amino acid metabolism pathways, particularly those related to aromatic amino acids, lysine, and branched-chain amino acids, were affected by the presence of specific NSLAB species, which differed between the two dairies. The results obtained in this study reveal the impact of starter culture on peculiar cheese microbiota assemblies, which selectively targets amino acid pathways, providing insights into the potential flavor and aroma characteristics of Asiago-PDO cheese.

Tuberculata Chang (Camellia L.): genomic features, comparative analysis, and phylogenetic relationships

BACKGROUND

Sect. Tuberculata belongs to Camellia, and its members are characterized by a wrinkled pericarp and united filaments. All the plants in this group, which are endemic to China, are highly valuable for exploring the evolution of Camellia and have great potential for use as an oil source. However, due to the complex and diverse phenotypes of these species and the difficulty of investigating them in the field, their complex evolutionary history and interspecific definitions have remained largely unelucidated.

RESULTS

Therefore, we newly sequenced and annotated 12 chloroplast (cp) genomes and retrieved the published cp genome of Camellia anlungensis Chang in sect. Tuberculata. In this study, comparative analysis of the cp genomes of the thirteen sect. Tuberculata species revealed a typical quadripartite structure characterized by a total sequence length ranging from 156,587 bp to 157,068 bp. The cp.genome arrangement is highly conserved and moderately differentiated. A total of 130 to 136 genes specific to the three types were identified by annotation, including protein-coding genes (coding sequences (CDSs)) (87-91), tRNA genes (35-37), and rRNA genes (8). The total observed frequency ranged from 23,045 (C. lipingensis) to 26,557 (C. anlungensis). IR region boundaries were analyzed to show that the ycf1 gene of C. anlungensis is located in the IRb region, while the remaining species are present only in the IRa region. Sequence variation in the SSC region is greater than that in the IR region, and most protein-coding genes have high codon preferences. Comparative analyses revealed six hotspot regions (tRNA-Thr(GGT)-psbD, psbE-petL, ycf15-tRNA-Leu(CAA), ndhF-rpl32, ndhD, and trnL(CAA)-ycf15) in the cp genomes that could serve as potential molecular markers. In addition, the results of phylogenetic tree construction based on the cp genomes showed that the thirteen sect. Tuberculata species formed a monophyletic group and were divided into two evolutionarily independent clades, confirming the independence of the section.

CONCLUSIONS

In summary, we obtained the cp genomes of thirteen sect. Tuberculata plants and performed the first comparative analysis of this group. These results will help us better characterize the plants in this section, deepen our understanding of their genetic characteristics and phylogenetic relationships, and lay the theoretical foundation for their accurate classification, elucidation of their evolutionary changes, and rational development and utilization of this section in the future.

Comparative chloroplast genomics of 24 species shed light on the genome evolution and phylogeny of subtribe Coelogyninae (Orchidaceae)

BACKGROUND

The orchids of the subtribe Coelogyninae are among the most morphologically diverse and economically important groups within the subfamily Epidendroideae. Previous molecular studies have revealed that Coelogyninae is an unambiguously monophyletic group. However, intergeneric and infrageneric relationships within Coelogyninae are largely unresolved. There has been long controversy over the classification among the genera within the subtribe.

RESULTS

The complete chloroplast (cp.) genomes of 15 species in the subtribe Coelogyninae were newly sequenced and assembled. Together with nine available cp. genomes in GenBank from representative clades of the subtribe, we compared and elucidated the characteristics of 24 Coelogyninae cp. genomes. The results showed that all cp. genomes shared highly conserved structure and contained 135 genes arranged in the same order, including 89 protein-coding genes, 38 tRNAs, and eight rRNAs. Nevertheless, structural variations in relation to particular genes at the IR/SC boundary regions were identified. The diversification pattern of the cp. genomes showed high consistency with the phylogenetic placement of Coelogyninae. The number of different types of SSRs and long repeats exhibited significant differences in the 24 Coelogyninae cp. genomes, wherein mononucleotide repeats (A/T), and palindromic repeats were the most abundant. Four mutation hotspot regions (ycf1a, ndhF-rp132, psaC-ndhE, and rp132-trnL) were determined, which could serve as effective molecular markers. Selection pressure analysis revealed that three genes (ycf1a, rpoC2 and ycf2 genes) might have experienced apparent positive selection during the evolution. Using the alignments of whole cp. genomes and protein-coding sequences, this study presents a well-resolved phylogenetic framework of Coelogyninae.

CONCLUSION

The inclusion of 55 plastid genome data from a nearly complete generic-level sampling provide a comprehensive view of the phylogenetic relationships among genera and species in subtribe Coelogyninae and illustrate the diverse genetic variation patterns of plastid genomes in this species-rich plant group. The inferred relationships and informally recognized major clades within the subtribe are presented. The genetic markers identified here will facilitate future studies on the genetics and phylogeny of subtribe Coelogyninae.

Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis

Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum. Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum, and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris. This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum.

Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome

Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.

People have the power. Electricity production, renewable energy transition, and communities empowerment across 11 Nordic-Baltic countries

Stakeholders and communities' involvement is vital for shaping novel intergenerational resource governance frameworks. This is crucial for modelling upcoming energy transitions towards cleaner and more sustainable production systems. New models envisage energy mixes in which renewable resources are prominent and offer sustainable development advantages. Examining electricity production figures is, hence, necessary to understand trends and formulate policies and actions. This paper aims at drafting the state-of-the-art of electricity production in the Nordic-Baltic Sea area, moving an exploratory regional appraisal. Aggregated and disaggregated data on electricity production sources are explored and compared for all the eleven selected countries-at domestic, sub-regional, and regional levels. The region shows great national diversity, which implies diversified energy policies. Thus, the role of local initiatives-such as power grid implementation-in local communities empowerment is revealed. From this outcome, possible strategies are prescribed locally to assist the regional sustainable energy appraisal and furnish indications for the European energy and ecological transition.

Postgraduate nurse education in Indonesia and Australia: A comparative analysis

BACKGROUND

Indonesia and Australia are neighbouring countries; however, their nursing systems are very different and there is limited migration between countries.

AIM

As part of a larger study, the aim was to undertake a comparative analysis of postgraduate nurse education in Indonesia and Australia.

DESIGN

Detailed literature review across academic and grey literature and semi-structured interviews with key stakeholders in Indonesia (n = 52) and Australia (n = 13) representing education, governments, professional nursing organisations, and rural, remote and urban health care providers.

FINDINGS

Three key categories of comparison were identified: Higher Education System, Education Offerings, and Specialist practice and education standards. Regulation of higher education was found to generally be comparable. Postgraduate nursing specialisations are available in both countries, but there are currently more offerings in Australia. Furthermore, nurse practitioner education and graduate entry pathways into nursing are only currently available in Australia. Journal publications are required for graduation from masters and doctoral programmes in Indonesia, but not Australia.

CONCLUSIONS

While there are many areas of similarity, postgraduate nurse education is more diverse in Australia, while there are growing opportunities for new developments in Indonesia. This analysis identifies areas for future consideration around postgraduate education development in both countries, along with possibilities for future collaboration. Furthermore, comparative analysis provided a useful foundation on mapping key elements.

Identification of transcriptionally active transposons in Barley

BACKGROUND

The genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants.

RESULTS

We analyzed the barley full-length cDNA (FLcDNA) sequences and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar 'Morex', seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3' untranslated region (3' UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of 'Morex' and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, 'Golden Promise' and 'Lasa Goumang'. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes.

CONCLUSION

We identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement and other research.

Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls

Background

Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods.

Methods

To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal.

Results

The number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods.

Conclusions

In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.

Nutritional value, elemental bioaccumulation and antioxidant activity of fruiting bodies and mycelial cultures of an unrecorded wild Lactarius hatsudake from Nanyue mountainous region in China

An unrecorded wild mushroom Lactarius hatsudake from Nanyue mountainous region in China was identified. Subsequently, comparative investigation on the nutritional value, elemental bioaccumulation, and antioxidant activity was performed in the fruiting body (FB) and mycelium (MY) samples of this species. It revealed that the contents of moisture (87.66 ± 0.16 g/100 g fw) and ash (6.97 ± 0.16 g/100 g dw) were significantly higher in FB, and the total carbohydrate, fat, and protein concentrations of FB were similar to those in MY. Among nutritionally important elements, FB possessed higher concentrations of potassium (37808.61 ± 1237.38 mg/kg dw), iron (470.69 ± 85.54 mg/kg dw), and zinc (136.13 ± 5.16 mg/kg dw), whereas MY was a better source of magnesium (1481.76 ± 18.03 mg/kg dw), calcium (2203.87 ± 69.61 mg/kg dw), and sodium (277.44 ± 22.93 mg/kg dw). According to the health risk estimation, FB might pose an aluminum-related health problem when a prolonged period of exposure, while MY was risk-free for consumers. The results of antioxidant capacity (1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) assays) in FB and MY were within the range of 104.19 ± 5.70 mg ascorbic acid equivalents (AAE)/g to 169.50 ± 4.94 mg AAE/g, and half maximal effective concentration EC50 values ranged from 0.23 ± 0.01 mg/mL to 0.62 ± 0.05 mg/mL. The aqueous extracts of MY demonstrated a strong ABTS radical scavenging capacity with the highest AAE value.

Decision-theoretic rough set model and spatial analysis-based waste-to-energy incineration plant site selection: a case study in first-tier cities of China

Selecting a sustainable waste-to-energy (WTE) incineration plant site is important for handling huge challenges created by on-going municipal solid waste. However, many studies with WTE incineration plant site problems fail to determine alternative evaluation criteria and cities beforehand, which may increase decision costs and evaluation risks. This paper proposes a novel methodology based on decision-theoretic rough set model and suitable analysis for selecting the optimal WTE incineration plant site. Firstly, from the features of cities, alternative evaluation criteria are determined by three-phase method. Considering different geographical features, a geographical index system is established. Secondly, subjective and objective criteria weights are determined by an improved DEMATEL (Decision Making Trial and Evaluation Laboratory) method and TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) method-based linear programming model under the hesitant fuzzy linguistic context, respectively. Subjective and objective criteria weights are combined to form the final criteria weights by building an optimization model. Thirdly, the decision-theoretic rough set model is utilized to select alternative WTE incineration plant sites. We utilize spatial analysis adopting Geographic Information System technology to rank all alternative cities to build facilities. Finally, a numerical case is performed to illustrate the feasibility of the proposed methodology. The sensitivity analysis with the parameter [Formula: see text] ranking from 0 to 1 is performed, the result confirms that the proposed methodology has better robustness. Compared with the multi-criteria decision-making methods, the effectiveness and superiority of the proposed methodology are demonstrated.

Assessing the Iran Health System in Making Progress towards Sustainable Development Goals (SDGs): A Comparative Panel Data Analysis

Background

Sustainable development goals' (SDGs) analysis can be caused a better understanding of factors contributing to access to health services and help shape policies to attain health goals. This review aimed to measure and compare the SDGs between Iran and selected categories.

Methods

This study was a comparative cross-sectional study. We identified indicators of health status based on the SDGs report 2019. The status of SDGs indicators was compared in Iran to four categories, including selected countries with similar social, economic, and health status, six regions of the WHO, the average of each income level group. SPSS 20 and Excel 2019 software were used for descriptive data analysis.

Results

The average life expectancy and healthy life expectancy were 75.7 years and 65.4 respectively in Iran. Iran's mortality rate in indicators named road traffic (32.1 per 100000 population), suicide (4.1 per 100000 population), and unintentional poisoning (1.2 per 100000 population) were higher than most of the categories. Iran's status in morbidity indicators had an approximately lower rate than all categories. Iran had full coverage in three immunization indicators like DTP3 immunization, MCV2 immunization, and PCV3 immunization, which was higher than all categories. Coverage of UHC in Iran (65%) was near to the global average (64%) and higher than the eastern Mediterranean Region (53%). Moreover, the prevalence of tobacco smoking (10.95%) and alcohol consumption (1%) were lower than global (6.4%) and the WHO regions (1.8%) average.

Conclusion

Health status measurement is a trend that requires the collection, processing, analysis, and dissemination of data by a set of indicators. There are several weaknesses in reported data in the SDGs for some indicators, the data collection process should be noticed seriously by policymakers.

Estimation of concrete materials uniaxial compressive strength using soft computing techniques

This study addresses a critical gap in concrete strength prediction by conducting a comparative analysis of three deep learning algorithms: convolutional neural networks (CNNs), gated recurrent units (GRUs), and long short-term memory (LSTM) networks. Unlike previous studies that employed various machine learning algorithms on diverse concrete types, our study focuses on mixed-design concrete and fine-tuned deep learning algorithms. The objective is to identify the optimal deep learning (DL) algorithm for predicting concrete uniaxial compressive strength, a crucial parameter in construction and structural engineering. The dataset comprises experimental records for mixed-design concrete, and models were developed and optimized for predictive accuracy. The results show that the CNN model consistently outperformed GRU and LSTM. Hyperparameter tuning and regularization techniques further improved model performance. This research offers practical solutions for material property prediction in the construction industry, potentially reducing resource burdens and enhancing efficiency and construction quality.

Genome-wide identification and analysis of the evolution and expression pattern of the SBP gene family in two Chimonanthus species

BACKGROUND

Chimonanthus praecox and Chimonanthus salicifolius are closely related species that diverged approximately six million years ago. While both C. praecox and C. salicifolius could withstand brief periods of low temperatures of - 15 °C. Their flowering times are different, C. praecox blooms in early spring, whereas C. salicifolius blooms in autumn. The SBP-box (SQUAMOSA promoter-binding protein) is a plant-specific gene family that plays a crucial vital role in regulating plant flowering. Although extensively studied in various plants, the SBP gene family remains uncharacterized in Calycanthaceae.

METHODS AND RESULTS

We conducted genome-wide identification of SBP genes in both C. praecox and C. salicifolius and comprehensively characterized the chromosomal localization, gene structure, conserved motifs, and domains of the identified SBP genes. In total, 15 and 18 SBP genes were identified in C. praecox and C. salicifolius, respectively. According to phylogenetic analysis, the SBP genes from Arabidopsis, C. praecox, and C. salicifolius were clustered into eight groups. Analysis of the gene structure and conserved protein motifs showed that SBP proteins of the same subfamily have similar motif structures. The expression patterns of SBP genes were analyzed using transcriptome data. The results revealed that more than half of the genes exhibited lower expression levels in leaves than in flowers, suggesting their potential involvement in the flower development process and may be linked to the winter and autumn flowering of C. praecox and C. salicifolius.

CONCLUSION

Thirty-three SBPs were identified in C. praecox and C. salicifolius. The evolutionary characteristics and expression patterns were examined in this study. These results provide valuable information to elucidate the evolutionary relationships of the SBP family and help determine the functional characteristics of the SBP genes in subsequent studies.

The impact of COVID-19 on hepatitis B and C virus prevention, diagnosis, and treatment in Bangladesh compared with Japan and the global perspective

AIM

This study aimed to assess the effect of COVID-19 on hepatitis-related services in Bangladesh and compared the situation with same study conducted in Japan and globally.

METHODS

We conducted an online cross-sectional questionnaire survey among the clinicians of four societies associated with liver disease in Bangladesh from October to December 2022. The questionnaire included the same questions as a survey conducted in Japan and globally.

RESULTS

A total of 83 clinicians from 8 divisions in Bangladesh participated; 66.3% were heads of departments/institutions. Except for HCV treatment initiation, more than 30% of clinicians reported a 76-99% decline in all services. Compared to Japan and the global survey, there was a significantly higher decline in all HBV and HCV services in Bangladesh. To resume services back to pre-COVID-19 levels, Patient anxiety and fear (Bangladesh Survey: 80.7% vs Japan Survey: 67.4% vs Global Survey: 37.9%, p < 0.0001), loss of space due to COVID-19 (Bangladesh Survey: 63.9% vs Japan Survey: 34.7% vs Global Survey: 19.4%, p < 0.0001) were the main challenges. As part of the mitigation strategy, usage of telemedicine (Bangladesh Survey: 83.1% vs. Japan Survey: 67.3% vs Global Survey: 78.6% p < 0.0001), COVID-19 benefits, such as increased laboratory testing platforms (Bangladesh Survey: 77.1% vs Japan Survey: 17.9% vs Global Survey: 41.8%, p < 0.0001) was reported significantly higher in Bangladesh than in Japan and global survey.

CONCLUSION

All the services-related to HBV and HCV were highly affected during greatest impact month of COVID-19 in Bangladesh and the decline level was higher than Japan and global survey. Repeated countermeasures of COVID-19 and constrained healthcare-system were the probable reasons in Bangladesh. Positive impact resulting from COVID-19 countermeasures should be utilized in the national hepatitis program in Bangladesh.

Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.)

BACKGROUND

The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.).

RESULTS

Here, the comprehensive identification and a comparative analysis of P450 superfamily members were conducted in cultivated and wild pear genomes. In total, 338, 299 and 419 P450 genes were identified in Chinese white pear, European pear and the wild pear, respectively. Based on the phylogenetic analyses, pear P450 genes were divided into ten clans, comprising 48 families. The motif and gene structure analyses further supported this classification. The expansion of the pear P450 gene family was attributed to whole-genome and single-gene duplication events. Several P450 gene clusters were detected, which have resulted from tandem and proximal duplications. Purifying selection was the major force imposed on the long-term evolution of P450 genes. Gene dosage balance, subfunctionalization and neofunctionalization jointly drove the retention and functional diversification of P450 gene pairs. Based on the association analysis between transcriptome expression profiles and flavonoid content during fruit development, three candidate genes were identified as being closely associated with the flavonoid biosynthesis, and the expression of one gene was further verified using qRT-PCR and its function was validated through transient transformation in pear fruit.

CONCLUSIONS

The study results provide insights into the evolution and biological functions of P450 genes in pear.

Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin

Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.

Towards standardization of human adipose-derived stromal cells secretomes

The secretome of adipose-derived stromal cells (ASC) is a heterogeneous mixture of components with a beneficial influence on cellular microenvironments. As such, it represents a cell-free alternative in regenerative medicine therapies. Pathophysiological conditions increase the therapeutic capacity of ASC and, with this, the benefits of the secretome. Such conditions can be partially mimicked in vitro by adjusting culturing conditions. Secretomics, the unbiased analysis of a cell secretome by mass spectrometry, is a powerful tool to describe the composition of ASC secretomes. In this proteomics databases review, we compared ASC secretomic studies to retrieve persistently reported proteins resulting from the most explored types of culturing conditions used in research, i.e., exposure to normoxia, hypoxia, or cytokines. Our comparisons identified only eight common proteins within ASC normoxic secretomes, no commonalities within hypoxic ASC secretomes, and only nine within secretomes of ASC exposed to proinflammatory cytokines. Within these, and regardless of the culturing condition that stimulated secretion, a consistent presence of extracellular matrix-related pathways associated with such proteins was identified. Confounders such as donors' age, sex, body mass index, the anatomical area where ASC were harvested, secretome collection method, data description, and how the data is shared with the scientific community are discussed as factors that might explain our outcomes. We conclude that standardization is imperative as the currently available ASC secretomic studies do not facilitate solid conclusions on the therapeutic value of different ASC secretomes.

Comparison of exergy and exergy economic evaluation of different geothermal cogeneration systems for optimal waste energy recovery

Since energy sources are limited, any activity aimed at recycling energy waste or facilitating energy conversion systems is invaluable. Against this background, most scientists focus on the integration of energy systems and the coupling of different technologies. In this study, a variety of power systems are investigated for optimal power conversion configurations of geothermal sources. Three configurations, Organic Rankine Cycle Geothermal Cooling (GPR/ORC), Kalina Cycle Geothermal Cooling (GPR/Kalina), and Rankine Cycle and Feed water Heater (GPR/FWH) Geothermal Cooling, are classified according to exergy and Study energy economic analysis. Calculations show that the GPR/FWH system has the highest net output power of 2963 kW. In addition, the GPR/Kalina system has the lowest output power and lowest energy efficiency among the systems launched. Across the three proposed systems, the fuel cell generates 1254 kW of electricity, while the Kalina cycle in the GPR/Kalina system generates 487 kW. Exergy studies show that the GPR/Kalina and GPR/FWH systems have the lowest and highest irreversibility (3795.4 kW and 4365.56 kW, respectively). Furthermore, the fuel cell was found to have the greatest exergy destruction rate among the three configurations. The results of the economic analysis show that the fuel cell has the highest cost ratio among all designs. In addition, the values of the dissipation factor show that the absorption chiller has the highest dissipation factor value among the three configurations. Furthermore, the comparative parametric analysis provides new aspects to introduce into the system.

The role of agricultural machinery in improving green grain productivity in China: Towards trans-regional operation and low-carbon practices

Agricultural machinery is effective in improving food production and labor productivity, but it also raises environmental concerns. The impacts of agricultural machinery on the green total factor productivity (GTFP) of grain in China are still under debate in the scientific literature. This study proposed an integrated framework for confronting this issue. The findings suggest that both agricultural mechanization and the GTFP of grain demonstrate a consistent upward trend with moderate fluctuations between 2001 and 2019. By expanding the spatial pattern, there is a positive spatial correlation between them. In addition, we compared the results in three grain functional areas by using the spatial Durbin model (SDM). There were significantly positive spatial spillover effects in major grain-producing areas, which were attributed to the trans-regional operation of agricultural machinery and its carbon reduction effects on neighboring provinces. Notably, the direct effects in major grain-marketing areas and producing-marketing balance areas were significantly positive because agricultural machinery has played a critical role in filling the gap in local labor shortages in grain production. Accordingly, adaptive strategies including building the "Internet + agricultural machinery operation" platform, implementing the land consolidation suitable for machinery, and developing low-carbon agricultural machinery should be fully considered by Chinese policy-makers to promote mechanized agriculture and a low-carbon economy. The findings of this study can help us better understand the role of agricultural machinery in improving green grain productivity in China and thus have significance for the modern and green transformation of agricultural production systems.

Ubiquitylome analysis reveals the involvement of ubiquitination in the cold responses of banana seedling leaves

Low temperature is a crucial environmental factor limiting the productivity and distribution of banana. Ubiquitination (Kub) is one of the main posttranslational modifications (PTMs) involved in plant responses to abiotic stresses. However, little information is available on the effects of Kub on banana under cold stress. In this study, we used label-free quantification (LFQ) to identify changes in the protein expression and Kub levels in banana seedling leaves after chilling treatment. In total, 4156 proteins, 1089 ubiquitinated proteins and 2636 Kub sites were quantified. Western blot assays showed that Kub was abundant in leaves after low-temperature treatment. Our results show that the proteome and ubiquitylome were negatively correlated, indicating that Kub could be involved in the degradation of proteins in banana after chilling treatment. Based on bioinformatics analysis, low-temperature stress-related signals and metabolic pathways such as cold acclimation, glutathione metabolism, calcium signaling, and photosynthesis signaling were identified. In addition, we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. Overall, our work presents the first systematic analysis of the Kub proteome in banana under cold stress and provides support for future studies on the regulatory mechanisms of Kub during the cold stress response in plants. SIGNIFICANCE: Banana is a typical tropical fruit tree with poor low-temperature tolerance,however, the role of PTMs such as Kub in the cold response of banana remains unclear. This study highlights the fact that the effects of low-temperature on proteome and ubiquitylome in the banana seedling leaves, we discussed the correlation between transcriptome and proteome, ubiquitylome and proteome, and we analyzed the expression and the changes of ubiquitination levels of low-temperature related proteins and pathway after chilling treatment, and we found that transcription factors and chromatin remodeling factors related to low-temperature stress were ubiquitinated. This study provides new insights into the ubiquitination pathway of banana under cold stress.

Identification, characterization, and comprehensive expression profiling of floral master regulators in pigeon pea (Cajanus cajan [L.] Millspaugh)

Pigeon pea is an important protein-rich pulse crop. Identification of flowering master regulators in pigeon pea is highly imperative as indeterminacy and late flowering are impediments towards yield improvement. A genome-wide analysis was performed to explore flowering orthologous groups in pigeon pea. Among the 412 floral orthologs identified in pigeon pea, 148 genes belong to the meristem identity, photoperiod-responsive, and circadian clock-associated ortholog groups. Our comparative genomics study revealed purifying selection pressures (ka/ks) on floral orthologs, and duplication patterns and evolution through synteny with other model species. Phylogenetic analysis of floral genes substantiated a connection between pigeon pea plant architecture and flowering time as all the PEBP domain-containing genes belong to meristem identity floral networks of pigeon pea. Expression profiling of eleven major orthologs in contrasting determinate and indeterminate genotypes indicated that these orthologs might be involved in flowering regulation. Expression of floral inducer, FT, and floral repressor, TFL1, was non-comparable in indeterminate genotypes across all the developmental stages of pigeon pea. However, dynamic FT/TFL1 expression ratio detected in all tissues of both the genotypes suggested their role in floral transition. One TFL1 ortholog having high sequence conserveness across pigeon pea genotypes showed differential expression indicating genotype-dependent regulation of this ortholog. Presence of conserved 6mA-methylation patterns in light-responsive elements and in other cis-regulatory elements of FT and TFL1 across different plant genotypes indicated possible involvement of epigenetic regulation in flowering.