Japanese encephalitis (JE) is a vaccine preventable disease caused by the Japanese encephalitis virus (JEV), which is primarily prevalent in Asia. JEV is a Flavivirus, classified into a single serotype with five genetically distinct genotypes (I, II, III, IV, and V). JEV genotype III (GIII) had been the most dominant strain and caused numerous out breaks in the JEV endemic countries until 1990. However, recent data shows the emergence of genotype I (GI) as a dominant genotype and it is gradually displacing GIII. The exact mechanism of this genotype displacement is still unclear. The virus can replicate in mosquito vectors and vertebrate hosts to maintain its zoonotic life cycle; pigs and aquatic wading birds act as an amplifying/reservoir hosts, and humans and equines are the dead end hosts. The important role of pigs as an amplifying host for JEV is well known. However, the influence of other domestic animals especially birds that live in high abundance and close proximity to human is not well studied. Here, we strive to briefly highlight the role of birds in JEV zoonotic transmission, discovery of birds as a natural reservoirs and amplifying host for JEV, species of birds susceptible to JEV infection, and the proposed effect of JEV on poultry industry in future perspective which have been neglected for a long times. We also discussed the recent in vitro and in vivo studies which show that the newly emerged GI viruses replicated more efficiently in bird-derived cells and ducklings/chicks than GIII, and an important role of birds in the JEV genotype shift from GIII to GI.

This study investigated the presence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples, collected from 843 groundwater wells suspected of contamination during 2007-2016, in Republic of Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%) and GI.1 (8.6%); 14 genotypes accounted for < 5.0%. Increasing HuNoV GII.17 has displayed a worldwide trend, including in Europe and Asia since 2010, and it was the dominant HuNoV genotype during 2013-2014 in Korea. However, HuNoV GII.4 was the major genotype detected in groundwater in Korea in 2015-2016, and it is becoming increasingly prevalent similar to HuNoV GII.17.

Dengue virus serotype 2 (DENV-2) is responsible for dengue epidemics on a global scale and is recognized for being associated with severe cases of the disease. This study conducted the phylogenetic investigation of DENV-2 in the Northern region of Brazil. DENV-2 isolates from 2017 to 2021, originating from Northern Brazilian states, were selected. Only one lineage (I) of the Asian-American genotype and one lineage (5) of the cosmopolitan genotype were observed. All sequences of the Asian-American genotype used in this study were segregated into a paraphyletic subgroup aligned with sequences from an American clade. These results indicate a probable geographic link starting from Puerto Rico. Additionally, sequences from Acre were identified and grouped into a monophyletic clade of the cosmopolitan genotype. These results indicate the cocirculation of two DENV-2 distinct lineages: Lineage 1, Asian-American genotype (probable origin from Puerto Rico); Lineage 5, cosmopolitan genotype (probable origin from Peru). Our results provide important data regarding the study of DENV genotypes and lineages distribution, as well as opening up possibilities for probable introduction and dissemination routes.

This study presents a novel approach to understanding evolutionary dynamics through topological analysis of genotypic structures. We model the genome of a simple organism as a topological torus undergoing mutations at a constant rate of 1% per generation. Employing persistent homology and other topological data analysis techniques, we investigate how these mutations influence the overall topology of the genomic structure over time. Our simulations reveal that specific critical mutations lead to significant changes in the homotopic and homologic properties of the torus. We interpret these topological shifts as potential markers for the formation of new subspecies. By identifying the precise points of topological "breaks" within the toroidal genomic representation, our model provides a quantitative framework for observing the incremental transformations that underpin major evolutionary developments. The results offer new insights into the thresholds of speciation and adaptation, demonstrating how gradual genetic changes can accumulate to produce qualitative shifts in organismal traits. This approach bridges the gap between microscopic genetic mutations and macroscopic evolutionary outcomes, potentially revolutionizing our understanding of evolutionary processes. Our findings have implications for various fields, including theoretical biology, genetic engineering, and conservation biology. The model provides a novel perspective on genetic resilience and adaptability, offering a foundation for future research on the relationship between genomic topology and evolutionary trajectories. It also emphasizes the innovative nature of the research and its potential impact on multiple fields of study.

INTRODUCTION There have been several advances in the treatment of hepatitis C virus (HCV) infection which have resulted in major reductions in the morbidity and mortality from liver-associated disease. These are not widely available in the Caribbean, due in part, to lack of knowledge of the epidemiology of infections with HCV. As efforts are made to eliminate HCV from the region, these and other existing barriers such as lack of an established database on HCV must be addressed. This review seeks to identify gaps in the knowledge of HCV in the Caribbean with respect to seroprevalence, genotype distribution and general epidemiologic characteristics. MATERIALS AND METHODS The literature for the period January 1, 2005, to October 2022, was reviewed to gather country specific data on HCV across the Caribbean. References were identified through indexed journals accessed through established databases. The usage pattern of HCV drugs was determined from data obtained from Pharmacists and Infectious Diseases Specialists across the region. RESULTS The prevalence of HCV in the Caribbean was 1.5%; the region should therefore be considered an area of moderate prevalence. Notably, data from specific countries were limited. The prevalence of HCV among intravenous drug users (21.9-58.8%); persons living with HIV/AIDS (0.8 to 58.5%); prisoners (32.8-64%) and men who have sex with men (MSM) (0.8-6.9%) was generally higher than in the general population (0.8-2.3%). Genotype 1 (83% was most prevalent followed by genotypes 2 (7.2%) and 3(2.1%), respectively. Drugs currently being used for treatment of HCV infections across the Caribbean include Epclusa (Sofosbuvir/velpatasvir), and Harvoni (Ledipasvir/sofosbuvir). Some of these drugs, are only available in the private sector and are sourced externally whenever needed. CONCLUSION There is a paucity of current data on the seroprevalence of HCV in the Caribbean and well-designed prospective studies are indicated to drive the implementation of treatment and control programs for HCV in the region. Barriers which need to be first overcome include unavailability and high cost of drugs used to treat HCV infections, injecting drug use and limited access to medical care and laboratory testing.

Poplar is a globalized commercial tree species that supports humanity's economy, energy, and ecology. To evaluate the twelve hybrid Populus euramericana genotypes developed in China, a total of six locations were selected for the test, comprising four climatic types and three soil kinds. The objective of this study is to characterize the early stages of Populus euramericana growth and test locations; to identify good genotypes for stable and high yield that may be encouraged; and to offer practical experience and technical assistance for further breeding of Populus euramericana. Main research methods include the statistical description of tree heights and diameter at breast heights[DBH], the establishment of a mixed effect model to analyze the genotype and environmental interaction effect [G×E], the use of best linear unbiased prediction[BLUP] values as GGE biplots to achieve visual screening, and the calculation of genetic parameters. Results show that the genotype effect [G], the environmental effect [E], and the G×E is significant; the BLUP value has a strong correspondence with the observed value; the goodness of fit of all biplots can explain more than 85% of the variation; broad-sense heritability of tree height and DBH is 0.13 and 0.3, type-B correlation is 0.36 and 0.65; G5, G7, G4 and G9 are excellent genotypes with high yield and stability; using these four genotypes tree height and DBH can get 3.35% and 0.81% genetic gains.The study concludes as follows: Rank-change interaction and scale-effect interaction were distinctly occurred. The G, E, and G×E all had a significant effect on the growth of poplar trees during their early stage. G4, G5, G7, and G9 genotypes have favorable development characteristics. N146 is a great source of paternal genetics.

Mucormycosis is known to be a rare opportunistic infection caused by Syncephalastrum species, which are Mucorales fungi of the Zygomycetes class. These moulds are rarely involved in clinical diseases and are generally seen as contaminants in the clinical laboratory. However, in recent years, case reports of human infections due to Syncephalastrum have increased, especially in immunocompromised hosts. In this study, we describe two new Syncephalastrum species, which were isolated from human nails and sputum samples from two different patients. We used several methods of genomic and phenotypic characterisation. The phenotypic analysis, relied on morphological features, analysed both by optical and scanning electron microscopy. We used Matrix Assisted Laser Desorption Ionization-Time of Flight mass spectrometry, energy-dispersive X-ray spectroscopy, and BiologTM technology to characterise the proteomic, chemical mapping, and carbon source assimilation profiles, respectively. The genomic analysis relied on multilocus sequence analysis of the rRNA internal transcribed spacers and D1/D2 large-subunit domains, and fragments of the translation elongation factor 1-alpha, and the β-tubulin genes. The two novel species in the genus Syncephalastrum, namely S. massiliense PMMF0073 and S. timoneanum PMMF0107, have a similar morphology to S. racemosum, but each display distinct phenotypic and genotypic features. The polyphasic approach, combining the results of complementary phenotypic and genomic assays, was instrumental in describing and characterising these two new Syncephalastrum species.

Knowledge of the genetic diversity of the available germplasm is an important foundation for crop conservation, management, and improvement. Successful breeding strategies rely on a sound understanding of the genetic diversity of the crop germplasm. This study was conducted to evaluate and compare the genetic diversity of 49 soybean [Glycine max (L.) Merrill] genotypes using SSR markers as well as to evaluate parental potential of these genotypes in cultivar improvement. The bulk of the genotypes were developed in the national soybean breeding program in Zimbabwe between 1940 and 2013. The genetic diversity and relatedness were estimated using 30 SSR markers and produced 5 clusters that generally matched the pedigree information of the germplasm. The SSR analysis detected a total of 135 alleles. The polymorphic information content ranged from 0.10 to 0.77 with a mean of 0.45. The SSR primer, Satt012 was the most informative. The SSR marker analysis showed a wide genetic diversity in the germplasm. To date, there are no reports regarding the genetic diversity analysis of soybean germplasm in Zimbabwe. The genotypes, EL41 and EL7; EL41 and EL1; as well as EL41 and EL42 were the most divergent thus, indicating their potential use as parental lines in the genetic improvement of soybean in the region.

Thalassemia syndromes are common monogenic disorders that represent a significant global health issue. No systematic epidemiological and molecular investigations on thalassemias in Croatian population have been reported to date. This prospective study included 70 children with a presumptive diagnosis of thalassemia, and their 42 first-degree relatives. Molecular characterization was performed using direct sequencing and gap-PCR methods. We identified 46 (30 children and 16 first-degree relatives) β-thalassemia heterozygous carriers from 24 unrelated families, carrying eight different mutations and one hemoglobin variant. Five variants account for approximately 85% of all affected β-globin alleles: Hb Lepore-Boston-Washington (32,6%), HBB: c.93-21G&gt;A (19,6%), HBB:c.315+1G&gt;A (13,1%), HBB:c.92+1G&gt;A (10,9%), and HBB:c.92+6T&gt;C variant (8,7%). A need for more detailed genetic profiling of β-thalassemia carriers is emphasized since genetic modifiers can significantly impact their phenotype. Our study provides important new insights into the relevance of β-thalassemia heterozygosity in the pediatric clinical practice.

Exploiting the relationship between the nutritional properties of seeds and the genetic background, constitutes an essential analysis which contributes to broadening our knowledge regarding the control of the nutritional quality of seeds or any other edible plant structure. This constitutes an important aspect when aiming at improving the nutritional characteristics properties of crops, including those of Chenopodium quinoa Willd (quinoa) which is intended to be one of the main nutrient sources ensuring food security worldwide. Changes in the nutritional properties of quinoa seeds due to the influence exerted by the environment, the genotype, or their interaction, have been already described in previous works, but there is an important limitation in the analyses carried out, including the outcomes that can be translated into agronomical practices by which quality can be improved selecting the most adequate genotype. In the present study, several seed nutritional-related parameters from fifteen quinoa cultivars grown in a particular environmental context were analyzed aiming at targeting compounds that can be determinants of seed quality. Important agronomical and nutritional differences were found among cultivars such as distinct mineral or protein contents and seed viability. More importantly, our analyses revealed key correlations between seed quality-related traits in some cultivars, including those that relate yield and antioxidants or the germination rate. These results highlight the importance of considering the genotypic variation in quinoa when selecting improved quinoa varieties with the best nutritional characteristics for new cultivation environments.

Vitamin D receptor (VDR) is an important candidate gene in musculoskeletal phenotypes. Polymorphisms in VDR have been previously associated with several pathologies and muscular strength in athletes and elderly people, however literature reported contradictory results. The object of this research is to verify the association between the most studied VDR variants (rs2228570, rs7975232, and rs1544410) and the increase of muscle mass in elite young soccer players. A sample of 55 soccer players (15-18 years old) form a professional team was selected for this study. DNA was extracted by salting out method and polymorphisms were genotyped by PCR-RFLP, followed by 2% agarose gel electrophoresis. To test the effect of the three SNPs, logistic regression analysis was applied. Body composition was carried out through skinfold thickness method, and muscular area of arm and lower limb were calculated using Frisancho formulas. All three polymorphisms met Hardy-Weinberg equilibrium (p &gt; 0.05) and their frequencies fell within the worldwide variability. A significant correlation between rs1544410 and increase of calf muscle mass was observed. Individuals carrying A allele showed higher calf muscular mass than those carrying the G allele (p = 0.034). Moreover, haplotype analysis applied to the two SNPs in linkage disequilibrium (rs7975232 and rs1544410), showed that AG haplotype resulted negatively correlated to calf muscle area. In conclusion, we confirm an association between VDR polymorphisms and muscular mass that could encourage the genetic screening of VDR gene to identify a potential risk of injury and for individual nutritional interventions.

We hypothesize the possible route of introduction of the cosmopolitan DENV-2 genotype into Brazil through the border with Peru. The five sequences presented in this study create a geographical link with the three others sequences of this genotype already recorded on the continent.

Feline infectious peritonitis (FIP), caused by the feline coronavirus (FCoV), is a devastating dis-ease in cats. Based on its antigenicity, FCoV can be divided into two serotypes: FCoV-I and FCoV-II. Furthermore, according to its pathogenicity, FCoV can be divided into feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV). There are numerous factors that affect the pathogenesis of FIP, among which host immunity and viral genetics can play an es-sential role in the development of FIP. Owing to the lack of specific symptoms, existing individual diagnostic methods can only support the suspicion of FIP, and multiple diagnostic methods and test data need to be combined to make a diagnosis. Although there are still no effective FIPV vaccines or commercial drugs available in the market, various studies have shown that some compounds can be used for treatment. Therefore, FIP is no longer incurable in cats

Some genetic diseases (“digenic traits”) are due to the interaction between two DNA variants, which presumably reflects biochemical interactions. For example, certain forms of Retinitis Pigmentosa, a type of blindness, occur in the presence of two mutant variants, one each in the ROM1 and RDS genes, while occurrence of only one such variant results in a normal phenotype. Detecting variant pairs underlying digenic traits by standard genetic methods is difficult and is downright impossible when individual variants alone have minimal effects. Frequent Pattern Mining (FPM) methods are known to detect patterns of items. We make use of FPM approaches to find pairs of genotypes (from different variants) that can discriminate between cases and controls. Our method is based on genotype patterns of length two, and permutation testing allows assigning p-values to genotype patterns, where the null hypothesis refers to equal pattern frequencies in cases and controls. We compare different interaction search approaches and their properties on the basis of published datasets. Our implementation of FPM to case-control studies is freely available.

Vascular pathogens are the causal agents of main diseases threatening the health and growth of olive crops worldwide. The use of endophytic microorganisms represents a challenging and promising strategy for management of vascular diseases in olive. Although current research has been focused on analyzing the structure and diversity of the endophytic microbial communities inhabiting the olive xylem, the characterization of this ecological niche has been overlooked and to date remain unexplored, despite that the characterization of the xylem sap composition is essential to unravel the nutritional requirements of xylem-limited microorganisms. In this study, branches from plantlets and adult olive trees of cultivars ‘Picual’ and ‘Arbequina' were selected to characterize the chemical composition of olive xylem sap extracted using a Scholander pressure chamber. Metabolome and ionome analyses of xylem sap were performed by proton nuclear magnetic resonance (NMR) spectroscopy-based and by inductively coupled plasma with optical emission spectroscopy (ICP-OES), respectively. Olive xylem sap metabolites included a higher relative percentage of sugars (54.35%), followed by alcohols (28.85%), amino acids (8.01%), organic acids (7.68%) and osmolytes (1.12%). Within each of these groups, the main metabolites in the olive xylem sap were mannitol, ethanol, glutamine, acetate and trigonelline, whereas K and Cl- were the main element and inorganic anion, respectively. Metabolomic profile varied when comparing olive plant age and genotype. The levels of glucose, fructose, sucrose and mannitol, choline, B and PO43 were significantly higher in adult trees than in plantlets for both olive genotypes, whereas NO3- and Rb content showed the opposite behavior. On the other hand, levels of aspartate, phenylalanine and Na were significantly higher in ‘Picual’ than in ‘Arbequina’ whereas Fe showed the opposite behavior but only for adult trees. Non-supervised hierarchical clustering analysis separated xylem sap composition firstly according to the plant age and then by the olive cultivar. Supervised PLS-DA analysis revealed that B, ethanol, Fe, Fructose, glucose, mannitol, sucrose and Sr were the most significative compounds discriminating adult trees from plantlets, whereas asparagine, aspartate, glutamate and phenylalanine or aspartate, arginine, ethanol and Sr were the most contributory compounds in the discrimination of both olive genotypes for adult trees or plantlets, respectively. Knowledge of the chemical composition of xylem sap will lead to a better understanding of the complex nutritional requirements of olive xylem-inhabiting microorganisms, including its vascular pathogens, and would allow the design of artificial growing media to improve culturing the olive microbiome.

Here we review and describe a set of research priorities to meet present and future challenges posed to farmed animal production that build on progress, successes and resources from the Functional Annotation of ANimal Genomes (FAANG) project.

Phenotype variation is produced through a complex of interactions between genotype and environment. Phenotype, genotype, and environment are addresses the relationship between architecture and identity. The term genotype biology and phenotype have been adopted into architecture in the late twentieth century. Genotypes are abstract relational models that govern the arrangement of space, and the principle of organizing space and phenotypes is the real realization of genotypes in the physical environment. The genotype is a reflection that is not only about the spatial organization but also the nature of social and cultural patterns. Then this study purpose to an understanding of the connectedness variant phenotype from a genotype and environment. The repetition pattern being stable structure in variation phenotype uses as a database to finding an identity in architecture. The method used in this research was Levi Strauss's structuralism and multi-layer of a biological system. This research samples traditional Malay houses in West Borneo, Indonesia. These houses have a unique site and existing environment. The houses can be found mainly along the river. The results found from the phenotype, genotype, and environment have value and meaning as a traditional Malay house rule in West Borneo which was always handed down from generation to generation.

Managing the multisystemic symptoms of type I Gaucher Disease (GD) requires a multidisciplinary team approach that includes disease-specific treatments, as well as supportive care. This involves a range of medical specialists, general practitioners, supportive care providers, and patients. Phenotype classification and the setting of treatment goals are important for optimizing the management of type I GD, and providing personalized care. The ability to classify disease severity using validated measurement tools allows the standardization of patient monitoring, and the measurement of disease progression and treatment response. Defining treatment goals is useful to provide a benchmark for assessing treatment response, and managing the expectations of patients and their families. Although treatment goals will vary depending on disease severity, they include the stabilization, improvement or reversal (if possible) of clinical manifestations. Enzyme replacement therapy (ERT) is the standard care for patients with type I GD, but a novel substrate reduction therapy (SRT), Eliglustat has demonstrated safety and efficacy in selected patients. To ensure that treatment goals are being achieved, regular, comprehensive follow up is necessary.

Considering the worldwide impact of heart failure, it is crucial to develop approaches that can help us comprehend its root cause and make accurate predictions about its outcome. This is essential for lowering the suffering and death rates connected with this widespread illness. Cardiomyopathies frequently result from genetic factors, and the study of heart failure genetics is advancing quickly. Dilated cardiomyopathy (DCM) is the most prevalent kind of cardiomyopathy, encompassing both hereditary and nongenetic abnormalities. It is distinguished by the enlargement of the left ventricle or both ventricles, accompanied by reduced contractility. The discovery of the molecular origins and subsequent awareness of the molecular mechanism is broadening our knowledge of DCM development. Additionally, it emphasizes the complicated nature of DCM and the necessity to formulate several different strategies to address the diverse underlying factors contributing to this disease. Genetic variations that can be transmitted from one generation to another can be a significant contributor to causing family or isolated DCM. Genetic variation also plays a significant role in determining susceptibility for acquired triggers for DCM. The genetic causes of DCM can have a diverse range of phenotypic expressions. It is crucial to select the most probable patients to have advantages from genetic testing. The purpose of this research is to emphasize the significance of identifying genetic DCM, the crucial relationships between genotype and phenotype, and the usefulness of genetic testing in the therapeutic care of both those affected and their relatives. This approach is expected to gain importance once treatment is guided by genotype-specific advice and disease-modifying medications.

The Genotype-Phenotype Working Group was established in November 2021 as part of the AgBioData Consortium (https://www.agbiodata.org) with the goal of identifying current challenges in annotating and integrating large-scale genotype and phenotype data. Over the course of the year, the members of this working group identified different types of data sets, explored experimental platforms and methods for data generation, and examined how these data are annotated including the metadata requirements. We conducted a thorough review of publicly funded repositories for raw and processed data for each data type. We also examined several secondary databases and knowledgebases that enable the integration of heterogeneous data types in the context of the Genome Browser, Pathway Networks and tissue-specific gene expression. The review revealed a need for additional infrastructural support, standards, and tools to connect Genotype to Phenotype data and enhance data interoperability for knowledge synthesis and to foster translational research.

The present study aimed to investigate influence of genotypic differences to zinc and iron agronomic biofortification responses among yield of finger millet. A field experiment was conducted over two seasons in farmers’ fields in Ethiopia (2019, 2020). The experimental design had 15 treatment combinations comprising 3 finger millet varieties and application of different combinations of zinc and iron mineral fertilizers. 5 soil-applied fertilizer treatments (20 kg h-1 FeSO4 + 25 kg h-1 ZnSO4 + NPKS, 25 kg h-1 ZnSO4 + NPKS, 20 kg h-1 FeSO4 + NPKS, NPKS, and 30% NPKS), at 2 locations (Gojjam and Arsi Negelle, Ethiopia), and two 2 slope positions (Foot and hill), replicated four times in a randomized complete block design. Grain yield and biomass were evaluated on plot basis. Plant height, total and productive tiller number, finger length of the longest spike and number of fingers per main ear were measured at maturity stage. The combined soil application of FeSO47H2O and ZnSO47H2O increased yield to Meba variety by 51.6%. Also, ZnSO47H2O fertilizer application increased yield to Urji variety by 27.6%. About 18.3% of yield enhancement of Diga-01 variety was achieved due to the FeSO47H2O fertilizers application. The findings of the present study suggests that the influence of Zn and Fe agronomic biofortification on yield of finger millet could be affected by genotype differences and environmental conditions.

The genotype by environment interaction (G×E) might have crucial impacts on the performance and fitness of agricultural species, such as Pacific white leg shrimp (Litopenaeus vannamei). This study explores how enhancements in management practices can counteract G×E effects on growth traits. We analysed a selectively bred population of white leg shrimp spanning the latest two generations, encompassing 259 full-sib and half-sib families with 40,862 individual shrimp measured for body weight and total length. Our analysis revealed moderate genetic correlations (0.60 – 0.65) between trait expressions in pond and tank environments, a significant improvement compared to earlier generations. Employing the average information-restricted maximum likelihood (REML) approach in mixed model analysis showed significant differences in heritability (h2) estimates between the two environments; however, the extent of these differences varied by trait (h2 = 0.68 in pond vs. 0.37 in tank for weight, and 0.41 vs. 0.67 for length). Our results indicate that G×E effects on growth traits in this population of L. vannamei were moderate but biologically significant. Consistent with our previous estimates in this population, genetic correlations between body weight and total length remained high (close to one) in pond and tank environments. Our findings collectively demonstrate that management improvements targeting stocking density, aeration, water quality, feeds, and feeding regimes mitigated the G×E effects on two economically significant traits in this population of white leg shrimp.

Porcine circovirus-associated diseases, caused by porcine circovirus type 2 (PCV2), are widespread and result in significant economic losses to the global swine industry. It is generally believed that PCV2 can be divided into nine genotypes (PCV2a to PCV2i), with the dominant being the PCV2d genotype. In this study, 2675 samples from pig farms in 13 cities in Jiangsu Province, China, were collected between 2014 and 2021 and subjected to polymerase chain reaction analysis to investigate the prevalence and genetic diversity of PCV2. The results showed that 41.42% (1108/2675) of samples tested positive for PCV2. The researchers further analyzed the genetic characteristics of 251 PCV2 strains and found that they belonged to the following four genotypes: PCV2a, PCV2b, PCV2d, and PCV2i. The dominant genotype was PCV2d, with a prevalence of 49.80% (125/251). The detection rate of PCV2b was significantly higher than those of PCV2a and PCV2i, at 35.46% (89/251), 7.57% (19/251), and 7.17% (18/251), respectively. We have further revealed the fingerprint of PCV2i genomic nucleotides for the first time. In conclusion, this study illustrates the high prevalence and evolutionary features of PCV2 in Jiangsu Province over the past few years.

Background: We evaluate the genetic and phenotypic features of a cohort of 12 Italian patients affected by Retinitis Pigmentosa (RP) associated with RP1 sequence variants.; Methods: Retrospective, single center study (Careggi Hospital, Florence), including a cohort of twelve Italian patients (Five male and seven female) affected by RP carrying pathogenic variants of the RP1 gene. A complete ophthalmic assessment and pedigree analysis was conducted with focus on the onset of disease symptoms, the patient’s age at the first diagnosis, the follow up duration and the possible presence of comorbidities; Results: The mean age at onset of symptoms was 31,0 ± 24,1 years old, with a mean follow-up period of 9,1± 2,4 years. The main symptoms at presentation were hemeralopia and visual field constriction. Fundus evaluation revealed a classic type of RP. Fundus autofluorescence (FAF), Optical Coherence Tomography (OCT), Electroretinogram (ERG), and visual field confirmed in most of the cases the typical features of classic retinitis pigmentosa.; (4) Conclusions: This single-center cohort of Italian patients provided information on the clinical and genetic features of RP1-associated RP. By comprehensively clarifying the genetic variations and their associated clinical manifestations, we can better tailor therapeutic interventions aimed at targeting specific genetic abnormalities. This ultimately promises to improve the prognosis and quality of life for individuals with RP-associated RP1.

Quinoa is a resilient crop known for its adaptability to diverse environmental conditions. This study examined the agronomic performance and ecological adaptability of quinoa across four distinct altitudes in the northwestern regions of China. Six quinoa genotypes were assessed for agronomic traits, phenology and yield performances, and nutritional quality characteristics in Yining city, Nilka County, Tekes County and Zhaosu County under varied environmental conditions. Our findings demonstrate significant variations in all measured traits including agronomic and nutritional quality traits across the various altitudes and genotypes. In Yining City, a warmer and lower altitude area, genotypes exhibit superior traits for fodder production, including increased branches, longer panicles, robust stems, and high seed protein content. Genotypes Jinli 1 and Beijing 2 achieve yields exceeding 3 tons per hectare (T/ha), highlighting the region’s productivity. Nilka and Tekes counties boasted the shortest quinoa crop cycles, with Jinli 1 yielding 4.05 T/ha seeds in Tekes County, exhibiting high protein and fat content alongside low saponins, making it prime location for yield production. Zhaosu County, with its cooler climate and fertile chernozem soil, elicited high 1000 seed weight and more robust protein response than Nilka and Tekes counties, illustrating the impact of soil fertility on nutritional composition. Correlation analyses further elucidated that the plants characterized by shorter flowering times, crop cycles, compact inflorescence, and taller heights exhibited superior seed yields. Our study contributes significant insights into the ecological adaptability and nutritional dynamics of quinoa, with implications for sustainable crop production and food security in diverse agroecosystems.

Background: Understanding the distribution of HPV types in cervical cancer cases is crucial for evaluating the effectiveness of HPV screening and vaccination in reducing cervical cancer burden. This study aimed to assess genotype prevalence among 178 cervical cancer cases detected during a 20-year screening period in Northern Norway and compare the potential efficacy of HPV vaccines in preventing cervical cancer. Methods: A total of 181 formalin-fixed paraffin-embedded (FFPE) tissue samples from women diagnosed with cervical cancer between 1995 and 2015 in Troms and Finnmark, Norway, were analyzed using a 45-type HPV DNA test. The results were compared to a 7-type HPV mRNA test targeting oncogenic types included in the nonavalent HPV vaccine. Results: Invalid HPV test results were observed in 1.7% (3/181) of the samples and were subsequently excluded from further analysis. Among the remaining cases, 92.7% (165/178) tested positive for HPV using any test combination. HPV DNA was detected in 159 cases (89.3%), while HPV mRNA was detected in 149 cases (83.7%). The most prevalent HPV types were 16 and 18, responsible for 70.8% of the cases, with the nonavalent vaccine types accounting for 86.6% of cases. HPV 35 was identified in eight cases (4.5%). Conclusion: The bivalent/quadrivalent HPV vaccines have the potential to prevent 76.4% (126/165) of HPV-positive cervical cancer cases, while the nonavalent vaccine could prevent 93.3% (154/165) of cases. Tailoring screening strategies to target HPV types with the highest oncogenic potential may improve cervical cancer detection and enable targeted interventions for high-risk individuals. The use of a 7-type HPV mRNA test holds promises as an advantageous approach.

Genotype imputation is widely used to enrich genetic datasets. The operation relies of panels of known reference haplotypes with typically whole-genome sequencing data. How to choose a reference panel has been widely studied and it is essential to have a panel that is well matched to the individuals who require imputation of missing genotypes. However, it is broadly accepted that such an imputation panel will have an enhanced performance with the inclusion of diversity; haplotypes from many different populations. We investigate this observation in this work by examining in fine detail exactly which reference haplotypes are contributing at different regions of the genome. This is achieved using a novel method of inserting synthetic genetic variation into the reference panel in order to track the performance of leading imputation algorithms. We show that while diversity may globally improve imputation accuracy, there can be occasions where incorrect genotypes are imputed following the inclusion of more diverse haplotypes in the reference panel. We however demonstrate a technique for retaining and benefitting from the diversity in the reference panel whilst avoiding the occasional adverse effects on imputation accuracy. What is more, our results elucidate more clearly the role of the diversity in a reference panel than has been shown in previous studies.

: Pearl millet (Pennisetum glaucum L) R. Br) is a subtropical grain and forage crop. It is privileged with several desirable forage attributes. Nevertheless, research on pearl millet is limited especially as a forage crop in the developing countries. Therefore, the objectives of this study were to investigate the field performance and stability of pearl millet genotypes for forage yield across seven environments. The study was conducted in seven environments (combination of locations and seasons) during 2016/2017-2018/2019 seasons. Twenty-five pearl millet genotypes, selected based on forage yield from a core collection of 200 accessions, were arranged in alpha lattice design with three replications. The parameters measured were fresh forage yield, days to flowering, plant height, number of culms m-2, leaf to stem ratio, and stem girth. The combined analysis revealed that environments, genotypes and their interaction had significant effects on all traits studied except the genotypic effect on stem girth. Across the seven environments, four genotypes (G14, G01, G12, and G22) out-yielded the check genotype in fresh matter yield by 20.7, 16.5, 11.0 and 9.8%, respectively. The additive main effects and multiplicative interaction (AMMI) analysis showed that the genotype, environment and their interaction were highly significant (P≤0.001) for fresh matter yield. The results of AMMI Stability Values (ASV) and the genotype selection index (GSI) combined with the AMMI estimate-based selection showed that genotypes G14, G22 and G01 were the most stable and adapted genotypes and were superior to the check genotype. These results indicate that forage pearl millet varieties could be developed directly through evaluation of the wealth available collections or indirectly through hybridization in crop breeding programs.

Accurate and robust methods are needed to monitor crop growth and predict grain yield and quality in breeding programs under variable agrometeorological conditions. Field experiments were conducted during two successive cropping seasons (2021, 2022) at four trial locations (Estonia, Latvia, Lithuania, Norway). The focus was on assessment of grain yield (GY), grain protein content (GPC), and UAV-derived NDVI measured at different plant growth stages. Performance and stability of 16 selected spring wheat genotypes were assessed under two N application rates (75, 150 kg N ha−1) and over contrasted agrometeorological conditions were assessed, and the quantitative relationships between agronomic traits and UAV-derived variables were figured out. None of the traits were subject to a significant (p&lt;0.05) genotype by nitrogen interaction. High-yielding and high-protein genotypes were detected with high WAASB stability, specifically under high and low N rates. This study highlights the significant effect of NDVI analysis on growth stages GS55 and GS75 as key linear predictors, especially in the context of spring wheat GY. However, the effect of these indices depends on the specific growing conditions in the respective locations, thus limiting their universal utility.

The inter-individual variability of CYP450s enzyme activity may be reduced by comparing the effects of bariatric surgery on CYP-mediated drug elimination in comparable patients before and after surgery. The current research will use a low-dose phenotyping cocktail to simultaneously evaluate the activities of six CYP isoforms and P-gp.The results showed that following weight reduction after surgery, the activity of all enzymes increased compared to the obese period, which was statistically significant in the case of CYP3A, CYP2B6, CYP2C9, and CYP1A2. Furthermore, the activity of P-gp after surgery decreased without reaching a statistical significance (p-value>0.05). Obese individuals had decreased CYP3A and CYP2D6 activity than the control group, albeit only CYP3A was statistically important. In addition, there was a trend to increase activity for CYP1A2, CYP2B6, CYP2C9, and CYP2C19 in obese patients compared to the control group, without reaching statistical insignificance (p-value≥0.05). After six months (at least), all enzymes and the P-gp pump activity were significantly higher than the control group except for CYP2D6.Ultimately, a greater comprehension of phenoconversion can aid in altering the patient's treatment. Further studies are required to confirm the changes in the metabolic ratios of probes after bariatric surgery to demonstrate the findings' clinical application. As a result, the effects of inflammation-induced phenoconversion on medication metabolism may differ greatly across persons and drug CYP pathways. It is essential to apply these results to the clinic to recommend dose adjustments.

Often yam varieties grown in different agro-ecologies show differential responses across production environments, a term known as genotype-by-environment interaction. Genotype-by-environment interaction makes selecting the best genotypes under varied production environments more complex. This study tested twenty yam genotypes evaluated in six test environments to assess genotype, environment, and the interaction between genotypes and environmental effect for tuber yield, yam mosaic virus, and dry matter content. The experiments were conducted in two seasons across three locations in Uganda using a randomized complete block design with three replications. The results showed a significant effect (p ≤ 0.001) for genotype (G), environment (E), and genotype by environment interaction for all the traits. Serere 2021 and Namulonge 2021 were identified as the most discriminating and representative environments for testing the yam mosaic virus, respectively. Serere 2021 was recognized as the most discriminating environment, whereas Arua 2021 was identified as the closest to an ideal environment for assessing yam tuber yields. The tested genotypes also exhibited high resistance to yam mosaic virus disease, high tuber yields, and high dry matter content. Genotypes UGY16020, UGY16034, UGY16042, and UGY16080 demonstrated great resistance to yam mosaic virus disease, high yielding, and considerable dry matter content and are thus potential parents for yam improvement. Further evaluation of the four genotypes should be done under farmers' production systems for selection, improvement, and release as new yam varieties for Uganda

To assess the genetic diversity of circulating dengue virus 2 in Senegal in 2018 we performed molecular characterization by complete genome sequencing and performing phylogenetic analysis. Sequenced strains belong to Cosmopolitan genotype of DENV-2 we observed intra-genotype variability leading to a divergence in two clades with differential geographic distribution. We report two variants namely; the “Northern variant” harbouring three nonsynonymous mutations (V1183M, R1405K, P2266T) located respectively on NS2A, NS2B and NS4A and the “Western variant” with two nonsynonymous mutations (V1185E, V3214E) located respectively in the NS2A gene and the NS5 gene. Findings calls for in depth in vitro and functional study to elucidate the impact of observed mutations on viral fitness, spread, epidemiology and disease outcome.

Somatic embryogenesis-mediated plant regeneration is essential for genetic manipulation of agronomically important traits in upland cotton. Genotype specific recalcitrance to regeneration is a primary challenge in deploying genome editing and incorporating useful transgenes into elite cotton germplasm. In this study, transcriptomes of a semi-recalcitrant cotton (Gossypium hirsutum L.) genotype ‘Coker312’ were analyzed at two critical stages of Somatic Embryogenesis that includes non-embryogenic callus (NEC) and embryogenic callus (EC) cells, and the results compared to a non-recalcitrant genotype ‘Jin668’. We discovered of 305 differentially expressed genes in Coker312, whereas, in Jin668, about 6-fold more genes (2,155) were differentially expressed. A total of 154 differentially expressed genes were common between the two genotypes. Gene enrichment analysis of upregulated genes identified functional categories such as lipid transport, embryo development, regulation of transcription, sugar transport, vitamin biosynthesis, among others. In Coker312 EC cells, five major transcription factors were highly upregulated: LEAFY COTYLEDON 1 (LEC1), WUS-related homeobox 5 (WOX5), ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and WRKY2. In Jin668, LEC1, BABY BOOM (BBM), FUS3, and AGAMOUS-LIKE15 (AGL15) were highly expressed in EC cells. We also found that gene expression of these embryogenesis genes was typically higher in Jin668 when compared to Coker312. We conclude that significant differences in expression of the above genes between Coker312 and Jin668 may be a critical factor affecting the regenerative ability of these genotypes.

Hepatitis B virus (HBV) can cause chronic infections, significantly increasing the risk of death from cirrhosis and hepatocellular carcinoma (HCC). A key player in chronic HBV infection is covalently closed circular DNA (cccDNA), a stable episomal form of viral DNA that acts as a persistent reservoir in infected hepatocytes and drives continuous viral replication. Despite the development of several animal models, few adequately replicate cccDNA formation and maintenance, limiting our understanding of its dynamics and the evaluation of potential therapeutic interventions targeting cccDNA. In this study, we aimed to develop a mouse model to investigate cccDNA formation and maintenance. We infected C57BL/6 mice with recombinant adeno-associated virus (rAAV) carrying a 1.3-overlength HBV genome (genotype C) and collected liver tissue at various time points to assess cccDNA levels and viral replication. Our results demonstrated the successful establishment of a chronic hepatitis B mouse model using rAAV-HBV1.3, which supported persistent HBV infection with sustained cccDNA expression in hepatocytes. Serum levels of HBsAg and HBeAg were elevated for up to 12 weeks, while alanine transaminase (ALT) levels remained within the normal range, indicating limited liver damage during this period. We confirmed HBV DNA expression in hepatocytes, and importantly, cccDNA was detected using qPCR after Plasmid-Safe ATP-Dependent DNase treatment, which selectively removes non-cccDNA forms. This established model provides a valuable platform for studying the long-term maintenance of cccDNA in chronic HBV infection and offers an important tool for testing novel therapeutic strategies aimed at targeting cccDNA.

Background: Hepatitis B virus (HBV), a lethal form of viral hapatitis, is an extra burden on the socioeconomic status of a country. Objectives: The population-based studies to quantify the incidence of hepatitis B. Data sources: in the North Waziristan, formally known as EX-FATA (Federal Administrated Tribal Area), Pakistan, are still rare. Study eligibility criteria: 943 individuals were selected on the basis of signs and symptoms to determine the epidemiology of HBV in the study population. Tests: Hepatitis B virus (HBV). Methods of data synthesis: Among these, 626 were male and 317 were female. All the HBV suspected individual were screened through ICT (Indirect Coombs Test) , ELISA (enzyme-linked immunosorbent assay) and RT-PCR (Re-verse transcription polymerase chain reaction). Results: The results obtained from the screening tests for HBV revealed that RT-PCR based results are more reliable and it indicated that HBV infection is more common in male 41 (6.54%) than female 15 (4.73%). The age range selected for the study was 1-75 years. Age wise analysis indicated that HBV is more prevalent among individuals of age group between 16 to 45 years. This age range also showed higher number of patients having either mild, moderate or elevated viral loads. The HBV genotype D was the most common, present in 62.5% patients. However, 16.07 % patients were having genotype U, 12.5 % genotype C, 8.92 % genotype A, and 7.14% had genotype B. Discussion: The questionnaire based investigation revealed that HBV was most prevalent among married individuals (64.6%), whereas least prevalent among individuals having HBV positive family member (1.4 %). The other risk factors contributed were history of dental procedures (57.8%), ear, nose, piercing, or tattooing and uses of un-disposable syringes (56.5%), transfusion of blood or plasma (42.9%), surgery (41.8%), frequent visits to barber shops (39.45%), and addiction of injectable drugs (38.1%). The current study is providing a clear picture of the alarming situation HBV transmission and emphasis on the need for more effective planing, strategies and policies for the control and prevention of HBV.

Drosophila melanogaster serves as a important research model both for genetic investigations and for the study of metal toxicity, facilitating the elucidation of physiological mechanisms comparable to those of human organisms. In our research, we evaluated the toxicity effect resulting from exposure to various concentrations of lead and copper on the prolificity rates throughout the life cycle (egg-adult) of four genotypes of Drosophila melanogaster: wild-type (control), white, brown, and white-vestigial. During our study, the prolificity rates were examined across three repetitions under the impact of exposure to concentrations of 0.50, 1.00, 2.00, and 4.00 mM of copper (CuSO₄) and lead (Pb(C₂H₃O₂₎₂). Prolificity rates throughout the life cycle exhibited variations as a direct consequence of genetic factors, the concentration of exposure, and the specific type of metal, either copper or lead. The mutant white-vestigial genotype revealed an IC₅₀ concentration for prolificity inhibition at lower doses of 2.00 mM for copper and 4.00 mM for lead, in contrast to the control genotype (wild-type), which exhibited an inhibition concentration rate >IC₅₀ of 4.00 mM only in the case of copper. Our results concluded that the (i) dose influences the prolificity rate in a directly proportional manner, (ii) comparative analyses between copper and lead revealed that copper displayed toxicity across all genotypes within the concentration range of 0.50 mM to 2.00 mM. In contrast, lead exhibited toxicity within the concentration range of 1.00 mM to 4.00 mM, highlighting a (iii) more acute toxicity characteristic in the case of copper. Thus, the results of this research reflect the importance of using Drosophila melanogaster as a genetic model in the comparative study of the interaction between genetic factors and the toxicity of metals, offering significant insights into monitoring their impact and defining the maximum permissible doses on organisms.

Genome-wide association studies (GWAS) have successfully revealed numerous susceptibility loci for obesity. PREDATORR study (2014) shows that in Romania, 34,6% of adults aged 20-79 y/o are overweight, 31,4% are obese with a high risk of cardiometabolic complications, a number that puts almost 67% of Romania's population in the abnormal weight group. Our study aims to investigate the current staus of genetic foundation in metabolic disease associated with obesity, applied to a pilot group of patients specifically examining the impact of known polymorphisms and their haplotype of six food intake-regulating genes: leptin (LEP), leptin receptor (LEP-R), serotonin receptor (5HTR2A), ghrelin (GHRL), neuropeptide Y (NPY) and fat-mass and obesity-associated (FTO) with the following polymorphisms: LEP A-2548G, LEPR A-223G, 5HTR2A G-1439A, GHRL G-72T, NPY T-29063C, FTO A-T and body mass index (BMI). A notable link between the LEP-2548 rs7799039 gene's AG genotype and the risk of obesity was observed, particularly pronounced in males aged 40-49, with an approximately sevenfold increased likelihood of obesity. The 5HTR2A rs6311 AA genotype was associated with a higher BMI, not statistically significant. The FTO rs9939609 gene's AA genotype emerged as a significant predictor of obesity risk. Besides these significant findings, no substantial associations were observed with the LEPR, 5HTR2A, GHRL and NPY genes. Haplotype association analysis showed a suggestive indication of GRGMLA (rs7799039, rs1137101, rs6311, rs696217, rs16139, rs9939609 sequence) haplotype with susceptibility effect towards obesity predisposition. Linkage disequilibrium (LD) analysis showed statistically significant associations between LEP and LEPR gene (p = 1e-04), LEP and GHRL gene (p = 0.0047), GHRL and FTO gene (p=0.03). The outcomes of this study, to our knowledge, one of the very few on the Romanian population, aimed to be a starting point for further research on the targeted interventional strategies to reduce cardiometabolic risks.

Breeding for low hydrogen cyanide (HCN) varieties is a major objective of programmes targeting boiled cassava food product. To enhance breeding for low HCN, knowledge on genetic variation and trait heritability is essential. In this study, 64 cassava clones established across four locations and evaluated for HCN using three HCN assessment methods; 1 to 9 scale, 0 ppm to 800 ppm scale and a quantitative assay based on spectrophotometer readings (HCN_Spec). Data were also collected on the weather variables precipitation, relative humidity, and temperature. Significant differences were observed among clones (P &lt; 0.001) and locations (p &lt; 0.001). There were also significant (p &lt; 0. 001) clone by environment interactions. Locations Arua and Serere posted higher HCN scores among clones and were associated with significantly higher (p &lt; 0.001) mean daily temperature (K) and lower relative humidity (%) across 12-hour and 18-hour intervals. Within locations HCN broad sense heritability estimates ranged 0.22 – 0.64 while combined location heritability estimates ranged 0.14 to 0.32. Relationships between the methods were positive and strong (R2 = 0.75 – 0.92). It is expected that the information herein will accelerate efforts towards breeding for low HCN cassava varieties.

Background and objectives: Since 2013, highly effective direct-acting (DAA) chronic hepatitis C (CHC) antiviral therapy became available, which has cure rates of over 95%. For choice of optimal CHC treatment, assessment of hepatitis C virus (HCV) genotype (GT) and liver fibrosis stage are necessary. Information about distribution of these parameters among CHC patients in Baltic states and especially in Ukraine is scarce. This study was performed to obtain epidemiological data regarding CHC GT and fibrosis stage distribution for better planning of resources and prioritization of patients for DAA drug treatment according to disease severity in high-income (Baltic states) and lower-middle income (Ukraine) countries. Materials and Methods: This was an epidemiological, retrospective, cross-sectional study that included 1451 CHC patients. Demographic and disease information from medical charts was collected for each patient during a single visit. Results: Most frequent suspected mode of viral transmission was blood transfusions (17.8%), followed by injection drug use (15.7%); however, in 50.9% of patients exact mode of transmission was not clarified. In Ukraine (18.4%) and Estonia (26%) transmission by the injection drug use was higher than in Lithuania (5%) and Latvia (5.3%). Distribution of HCV GT among patients with CHC was as follows: GT1 - 66.4%; GT3 - 28.1; and GT2 - 4.1%. The prevalence of GT1 was the highest in Latvia (84%), and the lowest in Ukraine (63%, p<0.001). Liver fibrosis stages were distributed as follows: F0 - 12.2%, F1 - 26.3%, F2 - 23.5%, F3 – 17.1% and F4 - 20.9%. Cirrhosis (F4) was more prevalent in Lithuanian patients (30.1%) than in Estonians (8.1%, p <0.001). Conclusions: This study contributes to the knowledge of epidemiological characteristics of HCV infection in the Baltic states and Ukraine. The data regarding the patterns of HCV GT and fibrosis stage distribution will be helpful for the development of national strategies to control HCV infection in the era of DAA therapy.

Hepatitis C virus (HCV) causes both acute and chronic disease of the liver that can lead to liver cirrhosis, cancer and liver failure. HCV is characterized by high genetic diversity and substantial variations in prevalence of specific HCV genotypes in different countries of the world. Many effective regimens of direct-acting antivirals (DAAs), including pan-genotypic, can successfully treat HCV infection. However, genotype-specific treatments for HCV are being actively employed in the national plans for elimination of HCV infection around the world. Evaluation of HCV genotype prevalence in a country is mandatory for successful implementation of the national plans for elimination of HCV infection and allocation of financial resources to DAAs most effecting for specific HCV genotypes prevalent in a country. Here, we analyzed HCV genotypes, subgenotypes and recombinants in 10,107 serum samples from patients with chronic HCV infection from all Federal districts of Russia collected in 2015-2017. This is the first, largest evaluation of HCV genotypes performed on samples from all territories of Russia, from its Central Federal district to the Far East. Moreover, we have updated retrospective epidemiological analysis of chronic and acute HCV infection in Russia in 2001-2021. We demonstrate that the incidence of acute HCV infection in Russia reduced from 16.7 cases per 100,000 population in 2001 to 0.6 cases per 100,000 population in 2021. The number of cases of chronic HCV infection decreased from 29.5 to 16.4 per 100,000 population during this period. HCV genotype analysis indicated that HCV genotype 1 dominates in Russia (53.6%). Genotypes 3 and 2 were detected in 35.4% and 7.8% of patients respectively. These proportions are virtually identical in all regions of Russia except for Far East, where HCV genotype 2 amounts only to 1%. HCV genotypes 1 and 2 are more widespread in women, while HCV genotype 3 in men. The highest frequency of identification of genotype 3 was found in the age group of 31-40 years old (44.9%, respectively), and genotype 1 was more prevalent in a group of over 70 years old (72.2%). The proportion of HCV genotype 2 is predominant among HCV-infected persons older than 40 years. Discriminating HCV genotype 2 and recombinant RF1_2k/1b, which are frequently misclassified, is important for successful antiviral treatment of such patients. For the first time, we demonstrate the countrywide prevalence of HCV RF1_2k/1b in different regions of Russia. HCV RF1_2k/1b amounts to 3.2% in the structure of HCV genotypes, reaching 30% among samples classified as genotype 2 by some commercial genotyping tests. The highest proportion of HCV RF1_2k/1b was detected in the north-west (60%), southern (41.6%) and central (31.6%) federal district. Its frequency in Far Eastern and North Caucasus Districts was ~ 14.3%. HCV RF1_2k/1b was not detected in the Volga, Ural and Siberian districts. To conclude, this is the first and most complete evaluation of HCV epidemiology and genotype/subgenotype distribution in Russia.

Branched-chain amino acid (BCAA) levels are associated with skeletal muscle cross-sectional area (CSA). Serum BCAA levels are enhanced by whey protein supplementation (WPS), and evidence in clinical populations suggests an association of single nucleotide polymorphisms (SNPs) with BCAA metabolite levels. It is not known whether the same SNPs are associated with the ability to catabolise BCAAs from exogenous sources, such as WPS. The present study investigated whether possessing a higher number of alleles associated with increased BCAA metabolites correlates with muscle fiber CSA of m. vastus lateralis in physically active participants, and whether any relationship is enhanced by WPS. Endurance-trained participants (n=75) were grouped by self-reported habitual WPS consumption and genotyped for 5 SNPs (PPM1K rss1440580, APOA5 rs2072560, CBLN1 rs1420601, DDX19B rs12325419, TRMT61A rs58101275). Body mass, BMI and fat percentage were significantly lower and muscle mass higher in the WPS group (n=22) compared to Non-WPS (n=53). The number of BCAA-increasing alleles was correlated with fiber CSA in the WPS group (r=0.75, p&lt;0.0001) and was stronger for fast-twitch fibers (p=0.001) than slow-twitch fibers (p=0.048). Similar results remained when corrected for multiple covariates (age, physical activity, meat and dairy intake). No correlation was found in the Non-WPS group. This study presents novel evidence of a positive relationship between BCAA-increasing alleles and muscle fiber CSA in athletes habitually consuming WPS. We suggest that a high number of BCAA-increasing alleles improves the efficiency of WPS by stimulation of muscle protein synthesis, and contributes to greater fiber CSA.

Drought stress imposes substantial constraints on the growth and production of wheat (Triticum aestivum L.), a globally important cereal crop that is essential for food security. To mitigate these adverse effects, researchers are intensifying their efforts to comprehend how different genotypes respond to drought stress, aiding in the development of sustainable breeding and management strategies. This review summarized past and recent research on genotype-dependent responses of wheat to drought stress, encompassing morphological, physiological, biochemical, molecular, genetic, and epigenetic reactions in plants. Screening of drought-affected features at early developmental stages can provide valuable insights into the adult growth stages that are closely linked to plant productivity. The review underscores the importance of identifying key traits associated with drought resistance, and the potential of leveraging wheat diversity to select cultivars with desirable agronomic characteristics. It also highlights recent advancements in investigating Bulgarian wheat genotypes with varying levels of drought tolerance, specifically in detecting essential features contributing to drought tolerance. Cultivating drought-resistant wheat genotypes and understanding stress stability determinants could markedly contribute to enhancing wheat production and ensuring stable yields under changing climate conditions.

Globally 390 millions of people are at risk of dengue infection; over the past 50 years the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases was noticed since 2017. In October 2018 an outbreak of DENV-2 was reported in Rosso area in the north of Senegal at the border with Mauritania. Out of the 187 blood specimen samples collected, 27 were positives by qRT-PCR and 8 were serologically positive for DENV IgM. Serotyping using qRT-PCR reveals that isolates were positive for DENV-2. A subset of DENV-2 positives samples was selected and subjected to full genome sequencing followed by phylogenetic analysis. Analysis of 06 nearly completed genome sequences (n= 6) revealed that isolates belong to the cosmopolitan genotype and are closely related to the Mauritanian strains detected between 2017 and 2018 and those detected in many West African countries such as Burkina Faso or Cote d’Ivoire. Our results suggest a transboundary circulation of the DENV-2 cosmopolitan genotype between Senegal and Mauritania and call for a need of coordinated surveillance of arboviruses between these two countries. Interestingly, high level of homology between West African isolates highlights endemicity and call for a set-up of sub-regional viral genomic surveillance which will lead to a better understanding of viral dynamic, transmission and spread across Africa.

The adverse relationship between viral hepatitis and pregnancy in developing countries was seen as a reflection of retrospective biased hospital-based data collection by the West. However, the discovery of HEV from an epidemic of non-A, non-B hepatitis in Kashmir and documenting increased incidence and severity of hepatitis E in pregnancy from a house-to-house survey unmasked the unholy alliance. Among the family of HEV’s, genotype (gt)-1, with a unique ORF4-encoded protein enhancing viral polymerase activity and viral replication, is the sole HEV that shows this adverse relationship. The epidemics caused by HEV-gt1 and not by HEV-gt2 show adverse relationship with pregnancy. The pathogenesis of the unholy alliance is complex and at present not well understood. Possibly multiple factors play a role in causing severe liver disease in the mother including: infection, replication and damage to the maternal-foetal interface by HEV-gt1; vertical transmission of HEV to foetus causing severe foetal/neonatal hepatitis; and combined viral and hormone related immune dysfunction of diverse nature in the mother promoting viral replication. Management is multidisciplinary and needs a close watch for the development and management of ALF. Preliminary data suggest beneficial maternal outcomes by early termination of pregnancy in patients with lower grades of encephalopathy.

Sorghum in Australia is grown in water-limited environments of varying extent, generating substantial genotype × environment interaction (GEI). Much of the yield variation and GEI results from variations in flowering time and tillering through their effects on canopy development. The confounding effects of flowering and tillering complicate the interpretation of breeding trials. In this study, we evaluated the impacts of both flowering time (DTF) and tillering capacity (FTN) on yield of 1741 unique test hybrids derived from three common female testers in 21 yield testing trials (48 tester/trial combinations) across the major sorghum production regions in Australia in three seasons. Contributions of DTF and FTN to genetic variation in grain yield were significant in 14 and 12 tester/trial combinations, respectively. The proportion of genetic variance in grain yield explained by DTF and FTN ranged from 0.2% to 61.0% and from 1.4% to 56.9%, respectively, depending on trials and genetic background of female testers. The relationship of DTF or FTN with grain yield of hybrids was frequently positive, but varied across the genetic background of testers. Accounting for the effects of DTF and FTN using linear models did not substantially increase the between trial genetic correlations for grain yield. The results suggested that other factors affecting canopy development dynamics and grain yield might contribute GEI and/or the linear approach to account for DTF and FTN on grain yield did not capture the complex non-linear interactions.

1) Background: We analyzed, by PET-SCAN, how growth hormone (GH) could act on the brain of an older woman, not GH-deficient, which was beginning to show some cognitive deficiencies and presented an ApoE genotype 4/3; 2) Methods: After performing a first psychometric study (TAVEC verbal learning test), the metabolic activity of brain structures related to knowledge, memory, and behavior was analyzed using 18-F Fluorodeoxyglucose PET-SCAN. The patient was then treated with GH (0.4 mg/day) for three weeks and on the last day under this treatment, a new PET-SCAN was performed. One month after beginning treatment with GH, a new TAVEC test was performed; 3) Results: GH administration normalized the cognitive deficits observed in the first psychometric test and increased significantly (P < 0.025) the metabolic activity in practically all brain cortical areas, specifically in the left hippocampus and left amygdala, although not in the left parahippocampus; and 4) Conclusions: This is the first study in which the positive effects of GH on cerebral metabolism have been visualized in a human patient. Our data confirm the positive effects of this hormone on cognition, memory and behavior in patients affected by mild cognitive impairments.

Minirhizotron tubes were installed to monitor root growth dynamics of mature Shiraz grapevines in a rootstock trial established in the hot climate Riverina region of New South Wales, Australia. The vertical root distribution and seasonal root growth dynamics of Shiraz on own-roots and Shiraz grafted on the rootstocks Ramsey, 140 Ruggeri and Schwarzmann was studied for five seasons across a seven-year period to a depth of 60 cm. New root production was significantly influenced by genotype, soil depth, season, growth stage and year. Soil moisture and soil tem-perature were monitored at 10, 30 and 60 cm in the last two seasons. Soil moisture at 30 cm and soil temperature at all three depths were significant predictors of root growth. New root numbers were significantly higher in 140 Ruggeri than the other rootstocks. To the depth studied, 140 Ruggeri roots were evenly distributed from the topsoil down, whereas the majority of roots of Schwarzmann and Shiraz were located at intermediate depths in the 10-40 cm ad 20-40 cm zones respectively, while Ramsey roots were found at 20 cm or below. Depending on genotype, root growth occurred across several phenological stages but tended to peak at flowering. In some years we observed root growth in early and late winter at rates exceeding that of autumn, and this was associated with warmer temperatures during this period. Overall, seasonal rooting dynamics were responsive to abiotic factors but dominated by genotype.

Human adenoviruses are one of the most important pathogens detected in acute respiratory diseases in pediatrics and immunocompromised patients. In 1953, Wallace Rowe described it for the first time in oropharyngeal lymphatic tissue. To date, more than 85 types of HAdV have been described, with different cellular tropisms. They can cause respiratory and gastrointestinal symptoms, even urinary tract inflammation, although most infections are asymptomatic. However, there is a population at risk that can develop serious and even lethal conditions. These viruses have a double-stranded DNA genome, 25-48 kbp, 90 nm in diameter, without a mantle, stable in the environment, and resistant to fat-soluble detergents. Currently the diagnosis is made with lateral flow immunochromatography or molecular biology through a polymerase chain reaction. The objective of this review is to recognize the variability of HAdV, the pandemic potential that a recombinant could present between HAdV-3 and 7 viral types, known to produce aggressive outbreaks in health facilities. The review determined the characteristics of HAdV, from the infection to treatment, vaccine development and the evaluation of the social determinants of health associated with HAdV, guiding the necessary measures for future sanitary control, and preventing disasters such as the SARS-CoV-2 pandemic.

The repeated application of herbicides has led to the development of herbicide resistance. Models are useful for identifying key processes and understanding the evolution of resistance. This study developed a spatially explicit model at a landscape scale to examine the dynamics of Lolium rigidum populations in dryland cereal crops and the evolution of herbicide resistance under var-ious management strategies. Resistance evolved rapidly under repeated herbicide use, driven by weed fecundity and herbicide efficacy. Although fitness costs associated with resistant plants re-duced resistance evolution, they did not affect the speed of spread. The most effective strategies to slow resistance involved diversifying cropping sequences (e.g., crop rotation) and the herbicide applications (e.g., rotating different herbicide modes of action). Pollen flow was the main disper-sal vector, with seed dispersal also contributing significantly. Strategies limiting seed dispersal effectively decreased resistance spread. However, the use of a seed-catching device at harvest could unintentionally enrich resistance in the area. It would be beneficial to optimise the move-ment of harvesters between fields. The model presented here is a useful tool that may assist in the exploration of novel management strategies within the context of site-specific weed management at the landscape scale, as well as in the advancement of our understanding of resistance dynamics.

Banana (Musa spp.) is an important crop to the economies of many developing countries. In the north of Argentina, a sub-tropical region, banana plants grow in a suboptimal environment that limits yield because only one harvest per year is achieved. The objective of this work was to characterize the agroecological aptitude of Formosa, Argentina, for banana production, through the behavior of three varieties of international use: Willians, Jafa and Gran Enano, evaluated during five consecutive campaigns. The three-way data analysis technique called Multiple Factor Analysis (MFA) was used for evaluating varieties’ performances across cycles of production. The results allowed inferring the existence of genotype x environment (GEI) interaction, corroborated by two-way factorial ANOVA. In order to determine how this suboptimal environment affects the development of each genotype of this perennial crop, Dual Multiple Factor Analysis (DMFA) was applied to jointly analyze the correlation structure among traits contributing to the performance of each variety at each campaign. The correlation structures between variables were different in each population and varied among campaigns. All traits showed a great variation across years and genotypes, the fruit peel thickness being the most discrepant throughout the campaigns. However, Formosa appeared as a promising subtropical agroecological environment to produce banana because varieties’ performances were acceptable for large scale production systems. In addition to evaluating the adequate aptitude for cultivating banana in Formosa considering the significant effect of GEI, this research makes a methodological contribution by proposing the use of three-way data analysis MFA and DMFA in Agronomy Science.

Hepatitis B Virus (HBV) is a challenge for global health services, affecting millions and leading hundreds to end-stage liver disease each year. This comprehensive review explores the interactions between HBV and the host, examining their impact on clinical outcomes. HBV infection encompasses a spectrum of severity, ranging from acute hepatitis B to chronic hepatitis B, which can potentially progress to cirrhosis and hepatocellular carcinoma (HCC). Occult hepatitis B infection (OBI), characterized by low HBV DNA levels in hepatitis B surface antigen-negative individuals, can reactivate and cause acute hepatitis B. The identification of diverse HBV genotypes reveals distinct geographical distributions and associations with clinical outcomes. Moreover, single nucleotide polymorphisms (SNPs) within the host genome have been linked to several clinical outcomes, including cirrhosis, HCC, OBI, hepatitis B reactivation, and spontaneous clearance. The immune response plays a key role in controlling HBV infection by eliminating infected cells and neutralizing HBV in the bloodstream. Furthermore, HBV can modulate host metabolic pathways involved in glucose and lipid metabolism and bile acid absorption, further influencing disease progression. HBV clinical outcomes correlate with three levels of viral adaptation. In conclusion, the clinical outcomes of HBV infection could result from complex immune and metabolic interactions between the host and HBV. These outcomes can vary among populations and are influenced by HBV genotypes, host genetics, environmental factors, and lifestyle. Understanding the degrees of HBV adaptation is essential for developing region-specific control and prevention measures.

This study was aimed to examine the recent trends of antibiotic resistance (AR) prevalence in Staphylococcus aureus isolated from milk of animals with clinical mastitis in areas of the Abruzzo and Molise regions in central Italy. Fifty-four S. aureus isolates could be obtained from routine testing for clinical mastitis agents carried out in the author institution in years 2021 and 2022. These were analyzed for phenotypic resistance to eight antibiotics recommended for testing by European norms and belonging to the antibiotic classes used for mastitis treatment in milk producing animals. Moreover, the presence of 14 transferable genetic determinants encoding resistance to the same antibiotics was analyzed by qPCR tests developed in this study. Phenotypic resistance to non-β-lactams was infrequent, with only one 2022 isolate resistant to clindamycin. However, low level resistance to the β-lactam cefoxitin was observed in 59.2% isolates in both years making these isolates classifiable as methicillin resistant. The AR genotypes detected were blaZ gene (50% 2021 isolates and 44.4% 2022 isolates), ermC/T- aphA3-blaZ (one 2021 isolate), ant6-ermC/T-aphA3-blaZ (one 2021 isolate), ermB-blaZ (one 2022 isolate) and mecA-mph (one 2022 isolate). An interview to the veterinarians who conferred the samples, regarding antimicrobials prescribed for mastitis treatment and criteria of usage, indicated a possible causal relation with the AR test results. The low prevalence of AR genotypes, not increasing in time, most probably reflecting the reported management of antibiotic therapies in farms. However, the frequently observed cefoxitin resistance needs to be explained genotypically, further monitored and limited by modifying antibiotic usage practices. The identification of a mecA positive isolate in 2022 suggests to investigate further if this genotype is emerging locally.

The association between angiotensin-converting enzyme insertion/deletion (ACE I/D) polymorphisms and plasma ACE levels may allow for the optimization of a preventive intervention to reduce cardiovascular morbidity and mortality in the chronic kidney disease (CKD) population. In this study, we aimed to analyze the association between ACE I/D polymorphism and cardiovascular mortality risk among non-hemodialyzed chronic kidney disease patients. This cross-sectional study examined 70 patients of Javanese ethnic origin with stable CKD who did not receive hemodialysis. ACE I/D polymorphisms, plasma ACE levels, atherosclerotic cardiovascular disease (ASCVD) risk, and cardiovascular mortality risk were investigated. As per our findings, the I allele was found to be more frequent (78.6) than the D allele (21.4), and the DD genotype was less frequent than the II genotype (4.3 vs. 61.4). The ACE I/D polymorphism had a significant direct positive effect on plasma ACE levels (path coefficient = 0.302, p = 0.021). Similarly, plasma ACE levels had a direct and significant positive effect on the risk of atherosclerotic cardiovascular disease (path coefficient = 0.410, p = 0.000). Moreover, atherosclerotic cardiovascular disease risk had a significant positive effect on cardiovascular mortality risk (path coefficient = 0.918, p = 0.000). The ACE I/D polymorphism had no direct effect on ASCVD and cardiovascular mortality risk. However, our findings show that the indirect effects of high plasma ACE levels may be a factor in the increased risk of ASCVD and cardiovascular mortality in Javanese CKD patients.

Methods for high-quality DNA extraction and knowledge of sex expression and flowering time are essential for applying genomic-assisted breeding and improve the success with hybridization in Guinea yam. A dioecious or monoecious pattern of flowering and sometimes non-flowering is a common phenomenon within and between the Dioscorea species. The flowering in yam plants raised from botanical seeds often takes an extended period, mostly till the first clonal generation after propagation from the tubers. The prolonged process of testing required to identify plant sex and flowering intensity in yam breeding often poses a challenge to realize reduced breeding cycle and apply genomic selection. This study assessed sample preservation methods for DNA quality during extraction and potential of DNA marker to diagnose plant sex at the early seedling stage in white Guinea yam. The predicted sex at the seedling stage was further validated with the visual score for the sex phenotype at the flowering stage. DNA extracted from leaf samples preserved in liquid nitrogen, silica gel, dry ice, and oven drying methods was similar in quality with a high molecular weight than samples stored in ethanol solution. Yam plant sex diagnosis with the DNA marker (sp16) identified a higher proportion of ZW genotypes (female or monoecious phenotypes) than the ZZ genotypes (male phenotype) in the studied materials with 74% prediction accuracy. The results from this study provided valuable insights on suitable sample preservation methods for quality DNA extraction and the potential of DNA marker sp16 to predict sex in white Guinea yam.

Bacterial wilt (BW), caused by Ralstonia solanacearum is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line ‘Hawaii 7996’ (H7996) is a stable and robust resistance source against various R. solanacearum strains. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1,604 SNP markers with an average distance of 0.82 cM was developed for 188 F9 recombinant inbred lines derived from the cross H7996 × WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I or/and race 3-phylotype II strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC3F3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P < 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P < 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P < 0.01) was confirmed and markers for this QTL have already been made available previously.

As a renewable industrial crop, Miscanthus offers numerous advantages, namely high photosynthesis activity (as a C4 plant) and exceptional CO2 fixation rate. These properties make Miscanthus very attractive for industrial exploitation, such as lignin generation. Here, we present a systematic study analyzing the correlation of the lignin structure with Miscanthus genotype and plant portion (stem versus leaf). Specifically, the ratio of the three monolignols and corresponding building blocks as well as the linkages formed between the units have been studied. Depending on the Miscanthus genotype and plant component (leaf versus stem), correlations between chemical structure and properties of the lignins have been determined, i.e. correlations in molecular weight, polydispersity and decomposition temperature. Lignin isolation was performed using non-catalyzed organosolv pulping and the structure analysis includes NREL, FTIR, UV-Vis, HSQC-NMR, TGA, pyrolysis GC/MS. Structural differences were found for stem and leaf-derived lignins. Compared to beech wood lignins, Miscanthus lignins possess lower molecular weight and narrow polydispersities (< 1.5 Miscanthus vs. > 2.5 beech) corresponding to improved homogeneity. In addition to conventional univariate analysis of FTIR spectra, multivariate chemometrics revealed distinct differences for aromatic in-plane deformations of stem versus leaf-derived lignins. These results emphasize the potential of Miscanthus as low-input resource and Miscanthus-derived lignin as promising agricultural feedstock.

Aimed to obtain purple garlic varieties, 360 bolting bulbs from the Protected Geographical Indication (PGI) “Las Pedroñeras” were selected for their size, and the presence of abundant external scales. After a further selection, 243 out of the 360 bulbs were discarded due to undesired characteristics, as light purple color, high number of small cloves, cloves affected by Fusarium spp. and mites, among other. It was stablished that each bulb would give rise to a family. Thus, 117 families were planted under a random design during season 2021-2022. Either physiological, morphological and phenological traits were assessed for each family, and the affectations by pest and pathogens were also controlled. After the assessment of this trial, 103 out 117 families remained in the program, and were used for the establishment of a second trial the next season. Unlike the first trial, after the evaluations only 23 families remained in the program. There was observed a high variability for most of traits, with a great influence of families. The phenotypic behavior of families was significative influenced by environment, highlighting the need of their assessment under different environmental conditions. The high variability registered for the target sample, opens the possibility to select new garlic varieties from this PGI.

The coffee plant is highly susceptible to drought, and different genotypes exhibit varying degrees of tolerance to low soil moisture. The current study aims to investigate the connection between drought tolerance and sensitivity in terms of seed traits, germination, and post-germination events, and their influence on the growth and physiology of young coffee plants. Two consecutive experiments were conducted to examine the impact of these factors. In the first experiment, germination performance was examined for three groups of coffee genotypes: relatively tolerant (Ca74140, Ca74112, and Ca74110), moderately sensitive (Ca74158, Ca74165, and CaJ-21), and sensitive (Ca754, CaJ-19, and CaGeisha). The subsequent experiment focused on the growth and physiological responses of two relatively tolerant (Ca74110 and Ca74112) and two sensitive (CaJ-19 and Ca754) genotypes under drought stress condition. The relatively tolerant genotypes showed quicker and more complete germination compared to other groups. This was associated with higher moisture content, higher seed surface area to volume ratio, and higher coefficient of velocity of germination, coefficient of variation of germination time, and germination index. Additionally, the relatively tolerant genotypes showed higher seedling vigor. The results of the second experiment demonstrated superior growth performance in relative tolerant genotypes compared to the sensitive groups. Young plants of coffee belonging to relatively tolerant genotypes exhibited higher growth performance than the sensitive genotypes, with a net assimilation rate strongly correlated to relative water content, leaf number, stomatal conductance, and chlorophyll-a. In addition, a strong correlation was exhibited between the growth of young coffee plants and the surface area to volume ratio of the seeds, as well as the germination percentage. The seedling vigor index showed a strong correlation with net assimilation rate, chlorophyll content, seedling growth, and cell membrane stability. Furthermore, principal component analysis illustrated distinct clustering of genotypes based on their germination and growth-physiological performance. Overall, the findings of this study suggest the importance of seed traits, germination, and post-germination events are integral factors in determining drought tolerance and sensitivity, as well as the growth and physiological responses of adult coffee plants.

The work is devoted to the investigation of virus quasispecies evolution and diversification due to mutations, competition for host cells, and cross-reactive immune responses. The model consists of a nonlocal reaction-diffusion equation for the virus density depending on the genotype considered as a continuous variable and on time. This equation contains two integral terms corresponding to the nonlocal effects of virus interaction with host cells and with immune cells. In the model, a virus strain is represented by a localized solution concentrated around some given genotype. Emergence of new strains corresponds to a periodic wave propagating in the space of genotypes. The conditions of appearance of such waves and their dynamics are described.

Maize is an important staple food crop in sub-Saharan Africa (SSA). However, the average grain yield on farmers’ fields falls considerably short of the demand of the region’s population. In addition, the normal endosperm maize widely consumed in SSA is deficient in vitamin A. Drought, a consequence of climate change, is a major constraint to maize production, resulting in seasonal low grain yield in farmers’ fields. The objectives of this study were to assess the performance of newly developed extra-early maturing provitamin A hybrids under managed drought and well-watered conditions, compare the outcomes of multiple trait base-index and multi-trait genotype-ideotype distance index selection procedures, and identify drought-tolerant hybrids with stable performance across contrasting environments for commercialization in SSA. One hundred and ninety provitamin A hybrids and six checks were evaluated under managed drought and well-watered conditions at Ikenne for two seasons between 2021 and 2023. A 14*14-lattice design was used for the field evaluations under both research conditions. Drought stress was achieved by the complete withdrawal of irrigation water 25 days after planting. Results revealed significant differences among the hybrids under drought and well-watered conditions. Grain yield, ears per plant, and plant aspect under managed drought were correlated to the same traits under well-watered conditions suggesting that the expression of these traits is governed by common genetic factors. Twenty-nine hybrids were identified as top-performing drought-tolerant hybrids by the multiple trait base index and multiple-trait genotype–ideotype distance index. Of the selected outstanding 29 hybrids, 34% were derived from crosses involving the tester TZEEIOR 197, demonstrating the outstanding genetic potential of this inbred line. Further analysis of the 29 selected hybrids revealed TZEEIOR 509 × TZEEIOR 197 as the hybrid that combined the most drought-tolerant adaptive traits. However, the hybrids TZEEIOR 526 × TZEEIOR 97, TZEEIOR 384 × TZEEIOR 30, TZEEIOR 515 × TZEEIOR 249, TZEEIOR 510 × TZEEIOR 197, TZEEIOR 479 × TZEEIOR 197, and TZEEIOR 458 × TZEEIOR 197 were identified as the most stable hybrids across drought and well-watered conditions. These hybrids should be extensively tested in multi-location trials for deployment and commercialization in SSA.

It has now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4,211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and genotypes. Our comprehensive biological characterization reveals that these PC subtypes are associated with different molecular mechanisms including unique cancer related signaling pathways, in which for most of the subtypes targeted treatment options are currently available. Some of the pathways we identified in all five PC subtypes, including cell cycle and the Axon guidance pathway are frequently seen and mutated in cancer. We also identified Protein kinase C, EGFR (epidermal growth factor receptor) signaling pathway and P53 signaling pathways as potential targets for treatment of the PC subtypes. Altogether, our results uncover the importance of considering both the mutation type and mutated genes in the identification of cancer subtypes and biomarkers.

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

Rotavirus species H (RVH) has been detected in pigs, humans and bats. Moreover, porcine RVHs have been recently identified in several swine-producing countries. Despite their zoonotic impact, genome information of RVHs is still limited. This study aimed to establish a tentative complete genome-based genotyping system for RVHs, by appending genomic sequences from 12 porcine RVHs identified in Japan between 2013 and 2015 to those from human and other porcine RVHs reported in previous studies. Phylogenetic analysis of 11 RNA segments indicated that porcine RVHs could be classified into multiple genotypes. Consequently, the genotype classification for RVHs revealed the existence of genotypes 10G, 6P, 6I, 3R, 4C, 7M, 6A, 2N, 4T, 6E, 3H for the genes VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Surprisingly, two distinctive types in NSP1 and NSP3 genes were identified from among the twelve porcine RVHs. Our data suggest a potentially novel gene rearrangement event between porcine RVH and rotavirus species C in the NSP3 gene. These findings would provide a new insight in understanding for evolution of RV.

Understanding the genotype x environment (GE) interaction for traget trait is valuable for growers, agronomists, breeders and the seed industry. The objective of this study was to see and explore the genotype x environment interaction for grain yield of wheat to better guide genotype selection and breeding. The genotype main effect and GE interaction effect (GGE) biplots resolved the following three genotypes: 85 (ETW17-377), 82 (ETW17-374) and 13 (ETW17-281) for being the best yielding and stable. The Kulumsa site planted on 4^th of July 2017 (environment 7=E7) and the DebreZeit site on 20^th of July 2017 (E3) were the most effective environments in distinguishing the test genotypes and are thus suitable environments for future evaluation and selection with specific adaptation. Melkasa site planted on 4^th July (E9) was a representative environment where genotypes can be evaluated for wide adpaptation. The genetic covariate biplot indicated that thousand kernel weight (TKW) and plant height (PH) had significant positive associations with grain yield implying the possible concurrent indirect selection of both traits for exploiting GE interaction for grain yield of wheat.

The majority of Candida species are known as non-pathogenic yeasts and rarely involved in human diseases. However, recently case reports of human infections caused by non-albicans Candida species have increased, mostly in immunocompromised hosts. Our study aimed to describe and caracterise as thoroughly as possible, a new species of the Candida genus, named here Candida massiliensis (PMML0037), isolated from a clinical sample of human sputum. We compared genetic data based on the sequences of four genetic regions: "Internal Transcribed Spacers" of rRNA, D1/D2 domains (28S large subunit rRNA) and part of the genes encoding Translation Elongation Factor 1-α and β-tubulin2, to morphological characters, from scanning electron microscopy (TM 4000 Plus, SU5000), physiological, including the results of oxidation and assimilation tests of different carbon sources by the Biolog system, and chemical mapping by Energy-Dispersive X-ray Spectroscopy. Lastly, the in vitro antifungal susceptibility profile was performed using the E-testTM exponential gradient method. The multilocus analysis supported the genetic position of Candida massiliensis (PMML0037) as a new species of the genus Candida, and the phenotypic analysis highlighted its unique morphological and chemical profile when compared to other Candida species included in the study.

Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have a unified engineering theory of evolution, we will neither be able to meet evolution’s potential as a design tool, nor understand or limit its unintended consequences on our designs. Our concept of the evotype offers a conceptual framework for engineering the evolutionary potential of biosystems. We show how a biosystem’s evolutionary properties might be rationally designed by engineering aspects of genetic variation, designed function, and natural selection. This idea could apply to all biosystems – from individual proteins to communities of whole-cells or even entire ecosystems – whether the goal is to direct evolution in the design process, or to limit its impacts during application. These principles could even be used beyond the realm of bioengineering to design entirely synthetic evolving auto-adaptive technologies.

Over 250 million people are infected chronically with hepatitis B virus (HBV), the leading cause of liver cancer worldwide. HBV persists due in part to its compact, stable minichromosome, the covalently-closed, circular DNA (cccDNA), which resides in the hepatocytes’ nuclei. Current therapies target downstream replication products, however, a true virological cure will require targeting the cccDNA. Finding targets on such a small, compact genome is challenging. For HBV, to remain replication-competent, it needs to maintain nucleotide fidelity in key regions, such as the promoter regions, to ensure that it can continue to utilize the necessary host proteins. HBVdb (HBV database) is a repository of HBV sequences spanning all genotypes (A-H) amplified from clinical samples, and hence implying an extensive collection of replication-competent viruses. Here, we analyzed the HBV sequences from HBVdb using bioinformatics tools to comprehensively assess the HBV core and X promoter regions amongst the nearly 70,000 HBV sequences for highly-conserved nucleotides and variant frequencies. Notably, there is a high degree of nucleotide conservation within specific segments of these promoter regions highlighting their importance in potential host protein-viral interactions and thus the virus’ viability. Such findings may have key implications for designing antivirals to target these areas.

Background: Tuberculosis (TB) manifests itself primarily in the lungs as pulmonary disease (PTB) and sometimes disseminates to other organs to cause extra-pulmonary TB, such as lymph node TB (LNTB). This study aimed to investigate the role of host genetic polymorphism in immunity related genes to find a genetic basis for such differences. Methods: Sixty-three, Single nucleotide polymorphisms (SNPs) in twenty-three, TB-immunity related genes including eleven innate immunity (SLCA11, VDR, TLR2, TLR4, TLR8, IRGM, P2RX7, LTA4H, SP110, DCSIGN and NOS2A) and twelve cytokine (TNFA, IFNG, IL2, Il12, IL18, IL1B, IL10, IL6, IL4, IL1RA, IL8 and TNFB) genes were investigated to find genetic associations in both PTB and LNTB as compared to healthy community controls. The serum cytokine levels were correlated for association with the genotypes. Results: PTB and LNTB showed differential genetic associations. The genetic variants in the cytokine genes (IFNG, IL12, IL4, TNFB and IL1RA and TLR2,4 associated with PTB susceptibility and cytokine levels but not LNTB (p &lt; 0.05). Similarly, genetic variants in LTA4H, P2RX7, DCSIGN and SP110 showed susceptibility to LNTB and not PTB. Pathway analysis showed abundance of cytokine related variants for PTB and apoptosis related variants for LNTB. Conclusions: PTB and LNTB outcomes of TB infection have a genetic component and should be considered for any future susceptibility and functional studies.

We analyzed the SARS-CoV-2 spike (S) protein amino acid sequence extracted from 11,542 viral genomic sequences submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database through April 27, 2020. Consistent with prior reports, we found a major S protein mutation, D614 to G614, that was represented in 56% of all the analyzed sequences. All other mutations combined were less than 10%. After parsing the data geographically, we found most of the Chinese patient samples showed D614 (97%). By contrast, most patient samples in many European countries showed G614 (51 to 88%). In the United States, the genotypic distribution in California and Washington was similar to Asian countries, while the distribution in other US states was comparable to Europe. We observed a dramatic increase in the frequency of G614 over time in multiple regions, surpassing D614 when both were present, suggesting G614 S protein virus outcompetes D614 S protein virus. To gain insight into the consequences of the D614G mutation, homology modeling using a multi-template threading mechanism with ab initio structural refinement was performed for a region of the S protein (S591 to N710) spanning the D614G mutation and the S1 furin cleavage site. Molecular models of this region containing D614 or G614 revealed a major difference in secondary structure at the furin domain (RRARS, R682 to S686). The D614 model predicted a random coil structure in the furin domain whereas the G614 model predicted an alpha helix. Critical residues in the cleavage domain of G614 model were found to better align with the PDB structure of a furin inhibitor. Thus, homology modeling studies suggest a potential mechanism whereby the D614G mutation may confer a competitive advantage at the furin binding domain that may contribute to the rise of the D614G SARS-CoV-2 mutant.

African swine fever virus (ASFV) continues to spread globally causing severe economic losses to the pig farmers. Vietnam licensed two live attenuated vaccines based on the ASFV strains ASFV-G-ΔI177L and ASFV-G-ΔMGF, to control the ongoing ASF outbreaks. In 2023, newly emerging highly virulent recombinant ASFV viruses containing genetic elements from both ASFV p72 genotype I and II (rASFV I/II) strains were reported from Northern Vietnam. This study evaluated if the two vaccine strains were able to protect the pigs against the emerging rASFV I/II strain VNUA/rASFV/TN1/23. Pigs vaccinated with ASFV-G-ΔMGF or ASFV-G-ΔI177L, when challenged with rASFV I/II, succumbed to the infection, or developed signs of chronic ASF. The findings from this study show that both vaccine strains that are licensed and used in Vietnam, are unlikely to protect pigs from the emerging highly virulent rASFV I/II strains. This complicates the ongoing efforts to control ASF in Asia and globally and emphasizes the urgent need for a novel vaccine that can effectively protect pigs from the rASFV I/II strains.

A mass mortality event of Asian seabass Lates calcarifer juveniles occurred in Zhuhai, the main Asian seabass cultured area in mainland China. The fish samples were pooled for pathogen identification and both high viral loads of ISKNV and NNV were detected by real-time microfluidic quantitative PCR. Immunohistochemistry and immunofluorescence showed that strong ISKNV signals were examined in spleen and liver, while strong NNV signals were detected in brain and eye. The multi-tissue homogenates were inoculated into MFF-1 cell and SSN-1 cell, respectively. After several viral passages, both ISKNV and NNV were purely isolated from each other, and designated as ASB-ISKNV-23 and ASB-NNV-23, respectively. The whole genome sequences of ASB-ISKNV-23 and ASB-NNV-23 were determined and annotated. The result showed that ASB-ISKNV-23 and ASB-NNV-23 are composed of 112,236 bp and 4,538 bp, respectively. Phylogeny analysis showed that ASB-ISKNV-23 belongs to ISKNV-II sub-genotype and ASB-NNV-23 belongs to RGNNV genotype. Collectedly, coinfection of ISKNV-II and RGNNV were firstly documented in mass mortality of Asian seabass in mainland China. Importantly, both ISKNV-II and RGNNV were purely isolated using two different permissive cell lines. Our study provides useful information for better understanding the complex pathogenesis regarding the coinfection with ISKNV and NNV in farmed fish.

Background and Aim. Since virus-related hepatocellular carcinoma (HCC) pathogenesis involves liver inflammation, therefore, post-hepatitis C virus (HCV) infection would be a cause for liver cirrhosis that would progress to HCC. Cytotoxic T cells (Tc) are known to be involved in post-HCV complications and HCC pathogenesis. The inhibitory checkpoint Leukocyte-Associated Immunoglobulin-like Receptor-1 (LAIR-1) is expressed on Tc. Therefore, we aimed to determine whether the Tc expression level of LAIR-1 is associated with HCC progression post-HCV and moreover, to evaluate LAIR-1 expression as a non-invasive biomarker for HCC progression in the context of liver cirrhosis post-HCV genotype 4 (G4) in Egyptian patients’ peripheral venous blood liquid biopsy. We studied LAIR-1 expression on Tc related to the progression of liver cirrhosis in a case-controlled study enrolled 64 patients with post-HCV G4-HCC and 37 patients with post-HCV G4-liver cirrhosis. Methods: LAIR-1 expression was analyzed by flow cytometry. Results: LAIR-1 expression on Tc and the percentage of Tc positive for LAIR-1 (LAIR-1+Tc %) were significantly higher in the post-HCV G4-HCC group compared to the post-HCV G4-liver cirrhosis