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With rising demand for effective and sustainable measures in wound healing researchers are compelled to explore diverse methods that combine folk medicine with existing wound care to double the impact. Hemigraphis colorata (Blume) H G Hallier, an exotic plant in the Acanthaceae family, is a perennial herb that has potential therapeutic benefits. In the present investigation, a comparative study was conducted between the effect of tender and mature leaf extracts of H. colorata as well as the differentially expressed genes of both leaves using four upstream primers and one downstream (HT11C) primer. The rate of cell migration was studied by creating a scratch wound in HaCaT monolayer culture. The finding indicated that the application of tender leaf extract resulted in a higher rate of wound closure, whereas the mature leaf extract led to a two-fold increase in the secretion of TGF-β protein, as measured by ELISA. This demonstrates the therapeutic effectiveness of tender leaf extract in promoting wound healing compared to mature leaf extract. Additionally, the results of DDRT-PCR unveiled a diverse range of differentially expressed genes, which were registered as molecular markers (ESTs) and did not show homology with any known gene sequences in the NCBI database. [ABSTRACT FROM AUTHOR]

OBJECTIVES Minimally invasive thymectomy is an accepted approach for early-stage thymic epithelial neoplasia, reducing pain and length of stay compared with open surgery. In this study, we compare robotic and video-assisted thymectomy to assess pathological resection status, overall and disease-free survival. METHODS Data were retrieved from the European Society of Thoracic Surgeons prospectively maintained thymic database. Eighty-two international centres were invited to participate in the ESTS registry. Thirty-seven centres agreed to take part. We included all patients who had undergone complete thymectomy for malignancy through a minimally invasive approach and excluded patients in whom complete data were not available. RESULTS Between October 2001 and May 2021, a total of 899 patients with thymic malignancy underwent minimal access surgical resection and were included in the study. A propensity matched analysis was conducted with interrogation of 732 patients. Median age was 55 years, and 408 (56%) patients were female. Propensity matched was performed with 1:1 matching for surgical approach (video assisted = 366, robot assisted = 366). Robot-assisted surgery conferred significantly lower odds of incomplete resection (R1; 0.203 95% CI 0.13–0.317; P  < 0.001). However, there was no difference in terms of overall and disease-free survival between the 2 techniques. CONCLUSIONS In this analysis, after adjusting for thymoma stage, the odds of incomplete surgical resection were higher in patients undergoing video-assisted surgery than robotic. However, there was no difference in overall or disease-free survival. With data maturation and increased follow-up, this would need repeat analysis and perhaps may provide more credence to the concept of a prospective randomized study to compare outcomes in thymic epithelial neoplasia by surgical approach with a standardized pathological work-up. [ABSTRACT FROM AUTHOR]

The article discusses the collaborative effort of the American Association for Thoracic Surgery (AATS), European Association for Cardio-Thoracic Surgery (EACTS), European Society of Thoracic Surgeons (ESTS), and Society of Thoracic Surgeons (STS) to establish a comprehensive methodology manual for developing clinical practice guidelines (CPGs). The document emphasizes the importance of evidence-based recommendations, rigorous validation, and continuous updates to ensure relevance and trustworthiness. It outlines the process of creating CPGs, including selecting writing committee members, conducting systematic literature reviews, formulating recommendations, achieving consensus through voting, and undergoing external validation before publication. The article also highlights the dissemination and implementation of CPGs, addressing gaps in knowledge, future perspectives, and the need for continuous learning and flexibility in guideline development. [Extracted from the article]

Background: Phlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas. Methods: In this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region. Results: The analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal. Conclusions: Elucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania–sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins. [ABSTRACT FROM AUTHOR]

Abstract Background Phlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas. Methods In this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region. Results The analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal. Conclusions Elucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania–sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins. Graphical Abstract

OBJECTIVES The optimal management for spontaneous pneumothorax (SP) remains contentious, with various proposed approaches. This joint clinical practice guideline from the ERS, EACTS and ESTS societies provides evidence-based recommendations for the management of SP. METHODS This multidisciplinary Task Force addressed 12 key clinical questions on the management of pneumothorax, using ERS methodology for guideline development. Systematic searches were performed in MEDLINE and Embase. Evidence was synthesised by conducting meta-analyses, if possible, or narratively. Certainty of evidence was rated with GRADE (Grading, Recommendation, Assessment, Development and Evaluation). The Evidence to Decision framework was used to decide on the direction and strength of the recommendations. RESULTS The panel makes a conditional recommendation for conservative care of minimally symptomatic patients with primary spontaneous pneumothorax (PSP) who are clinically stable. We make a strong recommendation for needle aspiration over chest tube drain for initial PSP treatment. We make a conditional recommendation for ambulatory management for initial PSP treatment. We make a conditional recommendation for early surgical intervention for the initial treatment of PSP in patients who prioritise recurrence prevention. The panel makes a conditional recommendation for autologous blood patch in secondary SP patients with persistent air leak (PAL). The panel could not make recommendations for other interventions, including bronchial valves, suction, pleurodesis in addition to surgical resection or type of surgical pleurodesis. CONCLUSIONS With this international guideline, the ERS, EACTS and ESTS societies provide clinical practice recommendations for SP management. We highlight evidence gaps for the management of PAL and recurrence prevention, with research recommendations made. Shareable Abstract This update of an ERS Task Force statement from 2015 provides a concise comprehensive update of the literature base. 24 evidence-based recommendations were made for management of pneumothorax, balancing clinical priorities and patient views. https://bit.ly/3TKGp9e [ABSTRACT FROM AUTHOR]

Background: Saffron (Crocus sativus) is high valued spice crop, but due to its sterile nature, the crop is propagated exclusively through corms. Thus, the genetic base of this crop is very narrow, however, frequency of phenotypic variability is observed; and suggested the potential role of epigenetics in saffron crop growth and development. Methods and results: To facilitate epigenetic studies in saffron, we developed 1525 methylation-specific PCR (MSP) markers using MethPrimer. For this purpose, we used 6767 EST sequences of saffron available on the NCBI database. We also mine CpG islands (2555) and found that 32.7% of EST sequences had CpG islands. Out of 1525 MSP markers developed during the present study, 725 covered the CpG islands and 800 were without CpG islands. PCR amplification was found successful for 82% of MSP markers. A preliminary analysis suggested that 53.7% of genomic sites were methylated and more prominent (60% methylations) in non-CpG island regions, although, more comprehensive studies are required to validate it further. Conclusions: The epigenetic resource developed during the present study will strengthen the epigenetic studies like epiQTL mapping, epiGWAS to explore the molecular mechanisms and genomic/epigenomic regions associated with phenotype; and further may be utilized for saffron improvement programs through epibreeding. [ABSTRACT FROM AUTHOR]

Background: Considerable production losses are caused by heat and drought stress in okra. Germplasm evaluation at genetic level is essential for the selection of promising genotypes. Lack of genomic information of okra limits the use of genetic markers. However, syntenic markers of some related family could be used for molecular characterization of major economic traits. Methods and results: Herein, 56 okra genotypes were evaluated for drought and heat tolerance. Sixty-one expressed sequence tags (ESTs) identified for heat and drought tolerance in cotton were searched from literature surveys and databases. The identified ESTs were BLAST searched into okra unigene database. Primers of selected okra unigenes were synthesized and amplified in all genotypes using standard polymerase chain reaction (PCR) protocol. Marker trait association (MTA) of the syntenic unigenes were identified between genotypic and phenotypic data on the basis of linkage disequilibrium Functional syntenic analysis revealed that out of these 61 cotton ESTs 55 had functional homology with okra unigenes. These 55 unigenes were used as markers for further analysis (amplification). Okra genotypes showed significance variations for all the physo-morphological parameters under heat and drought stress. Genotypes Perbhani Karanti, IQRA-III, Selection Super Green, Anmol and Line Bourd performed better under drought stress whereas genotypes Perbhani Karanti, IQRA-III, Green Gold, OK-1501 and Selection Super Green showed heat tolerance. Fifty markers showed amplification in okra. Fifty-six okra genotypes were clustered into three distinct populations. LD analysis has shown most significant linkage between markers Unigene43786 and Unigene3662. MTAs using MLM and GLM models revealed that 23 markers have significant associations (p < 0.05) with different traits under control and stressed conditions. Relative water content is associated with four markers (Unigene10673, Unigene99547, Unigene152901, and Unigene129684) under drought conditions. Whereas, Electrolyte leakage was associated with 3 markers (Unigene109922, Unigene28667 and Unigene146907) under heat stress. Conclusion: These identified unigenes may be helpful in the development of drought and heat tolerant genotypes in okra. [ABSTRACT FROM AUTHOR]

Phyllody in sesame (Sesamum indicum L.) is caused by the mollicute, and phytoplasma is often associated with floral malformations, affecting partial to complete sterility in those plants. The molecular basis for floral malformations in sesame remains largely unexplored. A comparative transcriptome study was performed between symptomatic (phytoplasma-infected) and asymptomatic (control) sesame plants by screening with phytoplasma-specific primers. The same-aged floral buds with undifferentiated floral organs were subjected to suppression subtractive hybridization (SSH) technique and a total of 525 expressed sequence tags (ESTs) comprising of unique and differentially expressed sequences were cloned. The differential ESTs cloned from Sesamum indicum-forward subtraction (SiFS) and Sesamum indicum-reverse subtraction (SiRS) were 240 and 285, respectively. The ESTs for metabolism and cellular and membrane transport were abundant in SiRS library, suggesting their upregulation in response to phytoplasma. Likewise, ESTs for chaperones and retroelements with a role in plant defense were identified in SiRS library alone, suggesting host defense activation in response to phytoplasma. On the contrary, seven ESTs involved in flower developmental process, viz., BEL1-like homeodomain protein, zinc finger protein CONSTANS-LIKE 13, polygalacturonase-like, STS14 protein, auxin transport protein BIG, glutaredoxin, and 26S proteasome non-ATPase regulatory subunit 8 homolog-A were detected in SiFS library alone, indicating their repression in phytoplasma-infected sesame. Conversely, genes with a role in negative floral regulation, two-component response regulator-like APRR1 and squamosa promoter-binding-like protein 1, were abundant in SiRS library alone, confirming a role of phytoplasma in expression of negative regulators of flower development. Further, these findings were validated by real-time quantitative polymerase chain reactions (qPCRs). [ABSTRACT FROM AUTHOR]

Genetic profiling of the biodiversity in cultivated crop plants is necessary to preserve important genes and utilize them in a breeding program. Cucumber is used as a model plant to study various characteristics of Cucurbitaceae. Its adaptation to a wide range of climatic conditions suggested analyzing the landraces. The present study was conducted to evaluate the differences, at the genetic level, among landraces spanning five continents. DNA extracted from fifty-six landraces selected from USDA germplasm bank to cover a global representative sample of world cucumber landraces was used for polymerase chain reaction using twenty-eight polymorphic expressed sequence tags simple sequence repeat (EST-SSR) markers. Twenty-eight EST-SSR markers covering all seven chromosomes yielded 98 bands with an average of 3.42 bands per marker. Polymorphic information content ranged from 0.00 (EC35) to 0.74 (EC17) with an average of 0.34. Six clusters provided an appropriate summary of the variation among the landraces, with the two largest groups including 32 (Asiatic) and 17 (European and American) landraces, respectively. Four small groups, three with two members, and one with one member (PI 525155-Egypt) were dissimilar to the two main groups. Landraces from the same region were often clustered together. Genetic similarity of the landraces was revealed by marker banding patterns. The locations of genetic diversity for cucumber landraces can be identified from this study., (© 2024. The Author(s).)

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of O. chinensis from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that O. chinensis is closely related to Ravenala madagascariensis . The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of O. chinensis and offer a theoretical foundation for its conservation strategies.

This study extends our prior research on drought responses in three date palm cultivars (Khalas, Reziz, and Sheshi) under controlled conditions. Here, we investigated their drought stress adaptive strategies under ambient environment. Under natural field drought conditions, three date palm cultivars experienced significantly (p ≤ 0.05) varying regulations in their physiological attributes. Specifically, chlorophyll content, leaf RWC, photosynthesis, stomatal conductance, and transpiration reduced significantly, while intercellular CO 2 concentration and water use efficiency increased. Through suppression subtraction hybridization (SSH), a rich repertoire (1026) of drought-responsive expressed sequence tags (ESTs) were identified: 300 in Khalas, 343 in Reziz, and 383 in Sheshi. Functional analysis of ESTs, including gene annotation and KEGG pathways elucidation, unveiled that these cultivars withstand drought by leveraging indigenous and multifaceted pathways. While some pathways aligned with previously reported drought resilience mechanism observed under controlled conditions, several new indigenous pathways were noted, pinpointing cultivar-specific adaptations. ESTs identified in three date palm cultivars were enriched through GSEA analysis. Khalas exhibited enrichment in cellular and metabolic processes, catalytic activity, and metal ion binding. Reziz showed enrichment in biological regulation, metabolic processes, signaling, and nuclear functions. Conversely, Sheshi displayed enrichment in organelle, photosynthetic, and ribosomal components. Notably, ca. 50% of the ESTs were unique and novel, underlining the complexity of their adaptive genetic toolkit. Overall, Khalas displayed superior drought tolerance, followed by Reziz and Sheshi, highlighting cultivar-specific variability in adaptation. Conclusively, date palm cultivars exhibited diverse genetic and physiological strategies to cope with drought, demonstrating greater complexity in their resilience compared to controlled settings., (© 2024. The Author(s).)

Taiwan harbors five endemic species of salamanders (Hynobius spp.) that inhabit distinct alpine regions, contributing to population fragmentation across isolated "sky islands". With an evolutionary history spanning multiple glacial-interglacial cycles, these species represent an exceptional paradigm for exploring biogeography and speciation. However, a lack of suitable genetic markers applicable across species has limited research efforts. Thus, developing cross-amplifying markers is imperative. Expressed sequence-tag simple-sequence repeats (EST-SSRs) that amplify across divergent lineages are ideal for species identification in instances where phenotypic differentiation is challenging. Here, we report a suite of cross-amplifying EST-SSRs from the transcriptomes of the five Hynobius species that exhibit an interspecies transferability rate of 67.67%. To identify individual markers exhibiting cross-species polymorphism and to assess interspecies genetic diversity, we assayed 140 individuals from the five species across 84 sampling sites. A set of EST-SSRs with a high interspecies polymorphic information content (PIC = 0.63) effectively classified these individuals into five distinct clusters, as supported by discriminant analysis of principal components (DAPC), STRUCTURE assignment tests, and Neighbor-joining trees. Moreover, pair-wise F ST values > 0.15 indicate notable between-cluster genetic divergence. Our set of 20 polymorphic EST-SSRs is suitable for assessing population structure within and among Hynobius species, as well as for long-term monitoring of their genetic composition., (© 2024. The Author(s).)

Wild edible plants are often found to be rich sources of nutrients and medicinally beneficial compounds with pharmacological activities. Gnetum gnemon is a nutritionally important plant and a popular food source in parts of Assam and North-East India. Various microRNAs (miRNAs) have been recently identified in many plants; how ever, there are no records of identification of miRNAs in any species of Gnetum. The prediction of miRNA-target associations in G. gnemon is an important step to facilitate functional genomics studies in this species. In the present study, all known miRNAs from plants available in public domain were used to search for the conserved G. gnemon miRNA homologues in publicly accessible expressed sequence tags (ESTs) in NCBI database. An aggregate of 20 new potential miRNAs belonging to two diverse miRNA families (miR399 and miR5021) were identified through a homology-based search by following stringent filtering criteria. To investigate the potential cross-king dom effects of the identified miRNAs, we further identified the putative target genes of G. gnemon miRNAs in hu man transcriptome and analyzed them against the NCBI non-redundant protein database. The KEGG analysis of the target genes indicated that these genes were involved in different metabolic pathways such as caffeine meta bolism, drug metabolism, and nitrotoluene degradation. The target genes of G. gnemon miRNAs in humans were found to be associated with various disorders of both hereditary and non-hereditary origin. These results could help to shed new light on understanding of miRNA-mRNAs functional networks in this species and its po tential use as a small RNA-based therapy against some human diseases.

RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

Main conclusion: Enhanced levels of endogenous melatonin in the root of wheat, mainly through the OMT1 gene, augment the antioxidant system, reestablish redox homeostasis and are associated with combined stress tolerance. A systems biology approach, including a collection of computational analyses and experimental assays, led us to uncover some aspects of a poorly understood phenomenon, namely wheat (Triticum aestivum L.) combined drought and salinity stress tolerance. Accordingly, a cross-study comparison of stress experiments was performed via a meta-analysis of Expressed Sequence Tags (ESTs) data from wheat roots to uncover the overlapping gene network of drought and salinity stresses. Identified differentially expressed genes were functionally annotated by gene ontology enrichment analysis and gene network analysis. Among those genes, O-methyl transferase 1 (OMT1) was highlighted as a more important (hub) gene in the dual-stress response gene network. Afterwards, the potential roles of OMT1 in mediating physiochemical indicators of stress tolerance were investigated in two wheat genotypes differing in abiotic stress tolerance. Regression analysis and correspondence analysis (CA) confirmed that the expression profiles of the OMT1 gene and variations in melatonin content, antioxidant enzyme activities, proline accumulation, H2O2 and malondialdehyde (MDA) contents are significantly associated with combined stress tolerance. These results reveal that the OMT1 gene may contribute to wheat combined drought and salinity stress tolerance through augmenting the antioxidant system and re-establishing redox homeostasis, probably via the regulation of melatonin biosynthesis as a master regulator molecule. Our findings provide new insights into the roles of melatonin in wheat combined drought and salinity stress tolerance and suggest a novel plausible regulatory node through the OMT1 gene to improve multiple-stress tolerant crops. [ABSTRACT FROM AUTHOR]

Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.

Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that "temporal synexpression" predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs.

Long non-coding RNAs (lncRNAs) is a class of eukaryotic transcripts with length of more than 200 bp. They contribute to the regulation of gene expressions involved in multiple processes including the skin cell proliferation, differentiation, and reconstruction of the secondary hair follicles (SHFs). In this study, firstly, we identified 16 putative lncRNAs from SHFs of cashmere goat based on the EST sequences from NCBI database. Secondly, we investigated their transcriptional pattern in SHFs of cashmere goat, and constructed their ceRNA regulatory networks. The RT-qPCR results showed four lncRNAs (lncRNA-475074, -052149, -052140, and -051789) were significantly up-regulated, and nine lncRNAs (lncRNA-711032, -475083, -475070, -052139, -052127, -052037, -051903, -051847, and -051804) were significantly down-regulatd in anagen SHFs of cashmere goat. CeRNA networks analysis revealed complex interactional relationship among lncRNAs, miRNAs and mRNAs. Further, the KEGG pathway enrichment was performed for the potential target genes of the identified lncRNAs based on bioinformatics technique, and the results indicated that differentially expressed lncRNAs directly or indirectly might regulate potential target genes. Our results from this study will provide a significant information for further exploring the functions and possible mechanisms of the identified lncRNAs in SHFs of cashmere goat. [ABSTRACT FROM AUTHOR]

BackgroundAnopheles sinensis is a major malaria vector in China and other Southeast Asian countries, and it is becoming increasingly resistant to the insecticides used for agriculture, net impregnation, and indoor residual spray. Very limited genomic information on this species is available, which has hindered the development of new tools for resistance surveillance and vector control. We used the 454 GS FLX system and generated expressed sequence tag (EST) databases of various life stages of An. sinensis, and we determined the transcriptional differences between deltamethrin resistant and susceptible mosquitoes.ResultsThe 454 GS FLX transcriptome sequencing yielded a total of 624,559 reads (average length of 290 bp) with the pooled An. sinensis mosquitoes across various development stages. The de novo assembly generated 33,411 contigs with average length of 493 bp. A total of 8,057 ESTs were generated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. A total of 2,131 ESTs were differentially expressed between deltamethrin resistant and susceptible mosquitoes collected from the same field site in Jiangsu, China. Among these differentially expressed ESTs, a total of 294 pathways were mapped to the KEGG database, with the predominant ESTs belonging to metabolic pathways. Furthermore, a total of 2,408 microsatellites and 15,496 single nucleotide polymorphisms (SNPs) were identified.ConclusionsThe annotated EST and transcriptome databases provide a valuable genomic resource for further genetic studies of this important malaria vector species. The differentially expressed ESTs associated with insecticide resistance identified in this study lay an important foundation for further functional analysis. The identified microsatellite and SNP markers will provide useful tools for future population genetic and comparative genomic analyses of malaria vectors.

Objectives: Haemaphysalis longicornis is the most important tick species in Japan and has a wide range of vector capacity. Due to its veterinary and medical importance, this tick species has been used as a model for tick/vector biological studies. To identify the key molecules associated with physiological processes during blood feeding and embryogenesis, full-length cDNA libraries were constructed using the fat body, hemocytes-containing hemolymph, midgut, ovary and salivary glands of fed females and embryos of the laboratory colony of parthenogenetic H. longicornis. The sequences of cDNA from the salivary glands had been already released. However, the related information is still poor, and the other expressed sequence tags have not yet been deposited. Data description: A total of 39,113 expressed sequence tags were obtained and deposited at the DNA DataBank of Japan. There were 7745 sequences from embryos, 7385 from the fat body, 8303 from the hemolymph including hemocytes, 7385 from the midgut, and 8295 from the ovary. The data, including expressed sequence tags from the salivary glands was summarized into Microsoft Excel files. Sharing this data resource with the tick research community will be valuable for the identification of novel genes and advance the progress of tick research. [ABSTRACT FROM AUTHOR]

Compared to cereal crops several legumes are less characterized at the genomic level and rightly referred as orphan crops. Transfer of knowledge between model and crop legumes allows development of orthologous pan-taxon genomic tools to benefit research on resource poor taxa. Here, we developed 278 intron flanking gene-specific markers by BLAST aligning pigeonpea (Cajanus cajan (L.) Millsp.) expressed sequence tags (ESTs) with complete genome sequence of barrel medic (Medicago truncatula). A random 192 PCR primer pairs representing loci across the haploid genome (n = 8) of barrel medic were tested on a few important members of legume family. The single copy amplification rates of 31.8% (peanut, Arachis hypogaea) to 77.6% (barrel medic) signifies the success of cross taxon primers and suggested their potential use in comparative legume genomics. Genetic diversity was assessed in 48 pigeonpea genotypes using 143 intron flanking markers which revealed 71 polymorphic markers with PIC values ranging from 0.04 to 0.45 with an average of 0.23 per marker. The PCR products of different varieties of pigeonpea, cowpea and chickpea were sequenced and aligned to find putative SNPs. Integration of these newly developed markers into genetic maps in resource poor legumes will not only aid in the map saturation but also in designing successful marker-assisted selection programmes. [ABSTRACT FROM AUTHOR]

A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for >7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the >1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.

Wild edible plants are often found to be rich sources of nutrients and medicinally beneficial compounds with pharmacological activities. Gnetum gnemon is a nutritionally important plant and a popular food source in parts of Assam and North-East India. Various microRNAs (miRNAs) have been recently identified in many plants; however, there are no records of identification of miRNAs in any species of Gnetum. The prediction of miRNA-target associations in G. gnemon is an important step to facilitate functional genomics studies in this species. In the present study, all known miRNAs from plants available in public domain were used to search for the conserved G. gnemon miRNA homologues in publicly accessible expressed sequence tags (ESTs) in NCBI database. An aggregate of 20 new potential miRNAs belonging to two diverse miRNA families (miR399 and miR5021) were identified through a homology-based search by following stringent filtering criteria. To investigate the potential cross-kingdom effects of the identified miRNAs, we further identified the putative target genes of G. gnemon miRNAs in human transcriptome and analyzed them against the NCBI non-redundant protein database. The KEGG analysis of the target genes indicated that these genes were involved in different metabolic pathways such as caffeine metabolism, drug metabolism, and nitrotoluene degradation. The target genes of G. gnemon miRNAs in humans were found to be associated with various disorders of both hereditary and non-hereditary origin. These results could help to shed new light on understanding of miRNA-mRNAs functional networks in this species and its potential use as a small RNA-based therapy against some human diseases. [ABSTRACT FROM AUTHOR]

Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer., (© 2024. The Author(s).)

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity ( H o  = 0.389, H e  = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia ., Competing Interests: The authors declare that they have no conflict of interest.

Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and in that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit. To test for similar intron function in animals, we performed an experimental test and comparative analyses for autoregulation among distantly related animal RPS9 orthologs. Overexpression of an exogenous RpS9 copy in Drosophila melanogaster S2 cells induced alternative splicing and degradation of the endogenous copy by nonsense-mediated decay (NMD). Also, analysis of expressed sequence tag data from distantly related animals, including Homo sapiens and Ciona intestinalis, revealed diverse alternatively-spliced RPS9 isoforms predicted to elicit NMD. We propose that multiple forms of splicing regulation among RPS9 orthologs from various eukaryotes operate analogously to translational repression of the alpha operon by S4, the distant prokaryotic ortholog. Thus, RPS9 orthologs appear to have independently evolved variations on a fundamental autoregulatory circuit.

BackgroundThe genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus.Methodology and principal findingsAs the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling.Conclusions/significanceWe have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Array of new targets for investigation as cancer therapeutics has great potential to grow as new splice-variants are identified and characterized in cancer cell-lines and tumor samples. Tumor-specific splice variants are being discovered at an increasing rate and their functions are also investigated in cancer progression. The tumor-specific splice variants whose expression patterns and activities are successfully characterized may become attractive targets for ablation or splicing modification. The extreme specificity of their expression suggests that a variant-specific treatment may allow for targeting of cancerous cells with minimal impact to healthy tissues. Clinical investigation of applying antisense oligonucleotides to down-regulate mRNAs that contribute to cancer cell survival and to modify splicing patterns in muscular dystrophy has shown promising results. These results show that antisense therapy may be applied effectively and safely in humans. As these treatment strategies continue to improve and novel tumor-specific splice-variants are identified, modification of splicing patterns will become an important field of investigation to develop more effective and safe cancer therapies.

Wheat stem rust caused by Puccinia graminis f. sp. tritici, can cause significant yield losses. To combat the disease, breeders have deployed resistance genes both individually and in combinations to increase resistance durability. A new race, TTKSK (Ug99), identified in Uganda in 1999 is virulent on most of the resistance genes currently deployed, and is rapidly spreading to other regions of the world. It is therefore important to identify, map, and deploy resistance genes that are still effective against TTKSK. One of these resistance genes, Sr13, was previously assigned to the long arm of chromosome 6A, but its precise map location was not known. In this study, the genome location of Sr13 was determined in four tetraploid wheat (T. turgidum ssp. durum) mapping populations involving the TTKSK resistant varieties Kronos, Kofa, Medora and Sceptre. Our results showed that resistance was linked to common molecular markers in all four populations, suggesting that these durum lines carry the same resistance gene. Based on its chromosome location and infection types against different races of stem rust, this gene is postulated to be Sr13. Sr13 was mapped within a 1.2-2.8 cM interval (depending on the mapping population) between EST markers CD926040 and BE471213, which corresponds to a 285-kb region in rice chromosome 2, and a 3.1-Mb region in Brachypodium chromosome 3. These maps will be the foundation for developing high-density maps, identifying diagnostic markers, and positional cloning of Sr13.

Genomic markers play an important role in tracing the flow of genetic causality of observable signals in animals and plants. In farm animals, the participation of male animals in the gene pool of subsequent generations are much higher than female animals and testes are the most important organs of the male reproductive system. This study was conducted to investigate simple sequence repeats (SSR) within the expressed sequence tags (ESTs) in order to classify the Bos taurus testis tissue’s genes for their relationship and specificity with related reproductive domains. A total of 48,549 publicly available EST sequences from cattle testis tissue downloaded from GenBank database, out of which, 10,237 sequences that their library made from testis tissue were extracted and specialized as the studied sequences using several searching tools and software. Across these selective sequences, 2,039 contigs, 5,097 singletons, and 153 SSRs were detected. EST-SSRs were subsequently evaluated using GenBank and categorized based on their functions in biological systems of dairy cattle. Investigation of these motifs showed that the identified EST-SSRs can be classified into 48 types that GT in dinucleotides and GCC in trinucleotides had the highest frequency. Annotation and gene ontology analysis revealed a relationship among 54 domains with the observed SSRs. Localization and characterization of such markers can help tracing the production of amino acids coded by identified repeats as shown in this study.

Helianthus tuberosus L., known as the Jerusalem artichoke, is a hexaploid plant species, adapted to low-nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 expressed sequence tags (ESTs) from an H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3), and at tuber physiological maturity (Tm), in “VR” and “K8-HS142”clones. The former was selected as an early tuberizing and the latter as a late-tuberizing clone. We quantified inulin and starch levels, and qRT-PCR confirmed the expression of critical genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady-state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.

BackgroundBlood feeding evolved independently in worms, arthropods and mammals. Among the adaptations to this peculiar diet, these animals developed an armament of salivary molecules that disarm their host's anti-bleeding defenses (hemostasis), inflammatory and immune reactions. Recent sialotranscriptome analyses (from the Greek sialo = saliva) of blood feeding insects and ticks have revealed that the saliva contains hundreds of polypeptides, many unique to their genus or family. Adult tsetse flies feed exclusively on vertebrate blood and are important vectors of human and animal diseases. Thus far, only limited information exists regarding the Glossina sialome, or any other fly belonging to the Hippoboscidae.ResultsAs part of the effort to sequence the genome of Glossina morsitans morsitans, several organ specific, high quality normalized cDNA libraries have been constructed, from which over 20,000 ESTs from an adult salivary gland library were sequenced. These ESTs have been assembled using previously described ESTs from the fat body and midgut libraries of the same fly, thus totaling 62,251 ESTs, which have been assembled into 16,743 clusters (8,506 of which had one or more EST from the salivary gland library). Coding sequences were obtained for 2,509 novel proteins, 1,792 of which had at least one EST expressed in the salivary glands. Despite library normalization, 59 transcripts were overrepresented in the salivary library indicating high levels of expression. This work presents a detailed analysis of the salivary protein families identified. Protein expression was confirmed by 2D gel electrophoresis, enzymatic digestion and mass spectrometry. Concurrently, an initial attempt to determine the immunogenic properties of selected salivary proteins was undertaken.ConclusionsThe sialome of G. m. morsitans contains over 250 proteins that are possibly associated with blood feeding. This set includes alleles of previously described gene products, reveals new evidence that several salivary proteins are multigenic and identifies at least seven new polypeptide families unique to Glossina. Most of these proteins have no known function and thus, provide a discovery platform for the identification of novel pharmacologically active compounds, innovative vector-based vaccine targets, and immunological markers of vector exposure.

BackgroundTsetse flies, vectors of African trypanosomes, undergo viviparous reproduction (the deposition of live offspring). This reproductive strategy results in a large maternal investment and the deposition of a small number of progeny during a female's lifespan. The reproductive biology of tsetse has been studied on a physiological level; however the molecular analysis of tsetse reproduction requires deeper investigation. To build a foundation from which to base molecular studies of tsetse reproduction, a cDNA library was generated from female tsetse (Glossina morsitans morsitans) reproductive tissues and the intrauterine developmental stages. 3438 expressed sequence tags were sequenced and analyzed.ResultsAnalysis of a nonredundant catalogue of 1391 contigs resulted in 520 predicted proteins. 475 of these proteins were full length. We predict that 412 of these represent cytoplasmic proteins while 57 are secreted. Comparison of these proteins with other tissue specific tsetse cDNA libraries (salivary gland, fat body/milk gland, and midgut) identified 51 that are unique to the reproductive/immature cDNA library. 11 unique proteins were homologous to uncharacterized putative proteins within the NR database suggesting the identification of novel genes associated with reproductive functions in other insects (hypothetical conserved). The analysis also yielded seven putative proteins without significant homology to sequences present in the public database (unknown genes). These proteins may represent unique functions associated with tsetse's viviparous reproductive cycle. RT-PCR analysis of hypothetical conserved and unknown contigs was performed to determine basic tissue and stage specificity of the expression of these genes.ConclusionThis paper identifies 51 putative proteins specific to a tsetse reproductive/immature EST library. 11 of these proteins correspond to hypothetical conserved genes and 7 proteins are tsetse specific.

Abstract Background Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia. Results Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop. Conclusions These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.

Rhizoctonia solani AG1-IA (R. solani AG1-IA) is a major soil-borne fungal pathogen of maize that causes significant yield losses in all maize-growing regions worldwide. The sclerotium produced by R. solani AG1-IA can overwinter in grass roots or diseased plants and infect crops the following year. The molecular mechanism underlying sclerotium formation in R. solani is poorly understood. In this study, we constructed the cDNA library of the R. solani AG1-IA pathogenic strain WF-9, from which 329 high-quality expressed sequence tags (ESTs) were obtained. Of the 250 clustered unigenes, 12 genes were selected for further expression analysis during the three stages of sclerotial growth (mycelium, initiation of sclerotium, and maturation of sclerotium). The results of expression analysis support the previously suggested roles of chitin synthase D and exo-beta-1,3-glucanase in facilitating sclerotial growth through preservation of water content and energy. In addition, cytochrome P450, NADPH oxidase, catalase (CAT), acyl-CoA oxidase 1 (ACOX1), mitogen-activated protein kinase (MAPK), mitogen-activated protein kinase HOG1 (HOG 1), and the G-protein α subunit play important roles in balancing reactive oxygen species (ROS) levels during sclerotial development. The findings of this study can help understand the molecular mechanism of sclerotial development further.

We describe a method for the highly efficient and precise targeted modification of gene trap loci in mouse embryonic stem cells (ESCs). Through the Floxin method, gene trap mutations were reverted and new DNA sequences inserted using Cre recombinase and a shuttle vector, pFloxin. Floxin technology is applicable to the existing collection of 24,149 compatible gene trap cell lines, which should enable high-throughput modification of many genes in mouse ESCs.

Genomic markers play an important role in tracing the flow of genetic causality of observable signals in animals and plants. In farm animals, the participation of male animals in the gene pool of subsequent generations are much higher than female animals and testes are the most important organs of the male reproductive system. This study was conducted to investigate simple sequence repeats (SSR) within the expressed sequence tags (ESTs) in order to classify the Bos taurus testis tissue's genes for their relationship and specificity with related reproductive domains. A total of 48,549 publicly available EST sequences from cattle testis tissue downloaded from GenBank database, out of which, 10,237 sequences that their library made from testis tissue were extracted and specialized as the studied sequences using several searching tools and software. Across these selective sequences, 2,039 contigs, 5,097 singletons, and 153 SSRs were detected. EST-SSRs were subsequently evaluated using GenBank and categorized based on their functions in biological systems of dairy cattle. Investigation of these motifs showed that the identified EST-SSRs can be classified into 48 types that GT in dinucleotides and GCC in trinucleotides had the highest frequency. Annotation and gene ontology analysis revealed a relationship among 54 domains with the observed SSRs. Localization and characterization of such markers can help tracing the production of amino acids coded by identified repeats as shown in this study. [ABSTRACT FROM AUTHOR]