MedT5SQL: a transformers-based large language model for text-to-SQL conversion in the healthcare domain.

Introduction: In response to the increasing prevalence of electronic medical records (EMRs) stored in databases, healthcare staff are encountering difficulties retrieving these records due to their limited technical expertise in database operations. As these records are crucial for delivering appropriate medical care, there is a need for an accessible method for healthcare staff to access EMRs. Methods: To address this, natural language processing (NLP) for Text-to-SQL has emerged as a solution, enabling non-technical users to generate SQL queries using natural language text. This research assesses existing work on Text-to-SQL conversion and proposes the MedT5SQL model specifically designed for EMR retrieval. The proposed model utilizes the Text-to-Text Transfer Transformer (T5) model, a Large Language Model (LLM) commonly used in various text-based NLP tasks. The model is fine-tuned on the MIMICSQL dataset, the first Text-to-SQL dataset for the healthcare domain. Performance evaluation involves benchmarking the MedT5SQL model on two optimizers, varying numbers of training epochs, and using two datasets, MIMICSQL and WikiSQL. Results: For MIMICSQL dataset, the model demonstrates considerable effectiveness in generating question-SQL pairs achieving accuracy of 80.63%, 98.937%, and 90% for exact match accuracy matrix, approximate string-matching, and manual evaluation, respectively. When testing the performance of the model on WikiSQL dataset, the model demonstrates efficiency in generating SQL queries, with an accuracy of 44.2% on WikiSQL and 94.26% for approximate string-matching. Discussion: Results indicate improved performance with increased training epochs. This work highlights the potential of fine-tuned T5 model to convert medical-related questions written in natural language to Structured Query Language (SQL) in healthcare domain, providing a foundation for future research in this area.

Scorpion Venom Antimicrobial Peptide Derivative BmKn2-T5 Inhibits Enterovirus 71 in the Early Stages of the Viral Life Cycle In Vitro.

Enterovirus 71 (EV71), a typical representative of unenveloped RNA viruses, is the main pathogenic factor responsible for hand, foot, and mouth disease (HFMD) in infants. This disease seriously threatens the health and lives of humans worldwide, especially in the Asia-Pacific region. Numerous animal antimicrobial peptides have been found with protective functions against viruses, bacteria, fungi, parasites, and other pathogens, but there are few studies on the use of scorpion-derived antimicrobial peptides against unenveloped viruses. Here, we investigated the antiviral activities of scorpion venom antimicrobial peptide BmKn2 and five derivatives, finding that BmKn2 and its derivative BmKn2-T5 exhibit a significant inhibitory effect on EV71. Although both peptides exhibit characteristics typical of amphiphilic α-helices in terms of their secondary structure, BmKn2-T5 displayed lower cellular cytotoxicity than BmKn2. BmKn2-T5 was further found to inhibit EV71 in a dose-dependent manner in vitro. Moreover, time-of-drug-addition experiments showed that BmKn2-T5 mainly restricts EV71, but not its virion or replication, at the early stages of the viral cycle. Interestingly, BmKn2-T5 was also found to suppress the replication of the enveloped viruses DENV, ZIKV, and HSV-1 in the early stages of the viral cycle, which suggests they may share a common early infection step with EV71. Together, the results of our study identified that the scorpion-derived antimicrobial peptide BmKn2-T5 showed valuable antiviral properties against EV71 in vitro, but also against other enveloped viruses, making it a potential new candidate therapeutic molecule.

Comparative genomics of N-acetyl-5-methoxytryptamine members in four Prunus species with insights into bud dormancy and abiotic stress responses in Prunus avium.

KEY MESSAGE: This study provides novel insights into the evolution, diversification, and functions of melatonin biosynthesis genes in Prunus species, highlighting their potential role in regulating bud dormancy and abiotic stresses. The biosynthesis of melatonin (MEL) in plants is primarily governed by enzymatic reactions involving key enzymes such as serotonin N-acetyltransferase (SNAT), tryptamine 5-hydroxylase (T5H), N-acetylserotonin methyltransferase (ASMT) and tryptophan decarboxylase (TDC). In this study, we analyzed Melatonin genes in four Prunus species such as Prunus avium (Pavi), Prunus pusilliflora (Ppus), Prunus serulata (Pser), and Prunus persica (Pper) based on comparative genomics approach. Among the four Prunus species, a total of 29 TDCs, 998 T5Hs, 16 SNATs, and 115 ASMTs within the genome of four Prunus genomes. A thorough investigation of melatonin-related genes was carried out using systematic biological methods and comparative genomics. Through phylogenetic analysis, orthologous clusters, Go enrichment, syntenic relationship, and gene duplication analysis, we discovered both similarities and variations in Melatonin genes among these Prunus species. Additionally, our study revealed the existence of unique subgroup members in the Melatonin genes of these species, which were distinct from those found in Arabidopsis genes. Furthermore, the transcriptomic expression analysis revealed the potential significance of melatonin genes in bud dormancy regulation and abiotic stresses. Our extensive results offer valuable perspectives on the evolutionary patterns, intricate expansion, and functions of PavMEL genes. Given their promising attributes, PavTDCs, PavT5H, PavNAT, and three PavASMT genes warrant in-depth exploration as prime candidates for manipulating dormancy in sweet cherry. This was done to lay the foundation for future explorations into the structural and functional aspects of these factors in Prunus species. This study offers significant insights into the functions of ASMT, SNAT, T5H, and TDC genes and sheds light on their roles in Prunus avium. Moreover, it established a robust foundation for further exploration functional characterization of melatonin genes in fruit species.

In Vivo DNA Assembly Using the PEDA Method.

Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage enzyme-assisted in vivo DNA assembly) method for direct in vivo assembly of individual DNA parts in multiple microorganisms, such as Escherichia coli, Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. PEDA allows in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and the efficiency is comparable to the prevailing in vitro DNA assembly, which will broadly boost the rapid progress of synthetic biology.

Correlation of Blomia tropicalis-specific immunoglobulin epsilon profiles with family history of atopy in a Filipino population.

Background: House dust mites are the major source of indoor allergens in the tropical and subtropical regions with Blomia tropicalis (Bt) allergens as one of the leading causative agents of sensitization among patients from the tropics. Despite the clinical importance of Bt in various populations, its allergenicity remains unclear among Filipino allergic patients. Objective: This study determined the sensitization profiles of allergic Filipinos against Bt allergens and its correlation with atopy. Methods: Total immunoglobulin epsilon (IgE) (n = 960), Bt-specific IgE (n = 247), and Blomia tropicalis 5 (Blo t 5)-specific IgE (n = 87) profiles of allergic and nonallergic subjects were measured through enzyme-linked immunosorbent assay (ELISA). Point-biserial correlation coefficient was used to determine the association between Bt-specific IgE levels and selected demographics. Inhibition ELISA was performed to measure the inhibition capacity of recombinant Blo t 5 (rBlo t 5) against Bt allergen extracts. Results: Mean total IgE levels of allergic cases (n = 171) were significantly higher (P < 0.001) compared to the mean IgE levels of nonallergic controls (n = 76). Among allergic subjects, 58% were sensitized to Blo t extract and 80% of which were sensitized to rBlo t 5 allergen. A positive correlation was observed between Bt-specific IgE and family history of atopic disease (P = 0.031). Inhibition assay revealed that 54% mean reactivity of 7 plasma samples was caused by rBlo t 5, validating that rBlo t 5 is a major allergen in Bt. Conclusions: This study has shown the importance of Bt as an allergen source that sensitizes atopic Filipino subjects. Hence, inclusion of Bt allergen extract and rBlo t 5 in the panel for allergy diagnosis and immunotherapy in Filipino populations is strongly recommended.

MiR-548t-5p regulates pancreatic ductal adenocarcinoma metastasis through an IL-33-dependent crosstalk between cancer cells and M2 macrophages.

IL-33 has been associated with pro- and anticancer functions in cancer. However, its role in pancreatic cancer metastasis remains unknown. This study aimed to explore the role of miR-548t-5p/IL-33 axis in the metastasis of pancreatic cancer. Luciferase activity assay, qRT-PCR, Western blot and ELISA were performed to prove whether IL-33 is the target of miR-548t-5p. In vivo metastasis assay and cellular transwell assay were performed to explore the role of miR-548t-5p/IL-33 axis in the invasion and metastasis of pancreatic cancer. Co-culture experiments and immunohistochemistry were performed to observe whether IL-33 affects cell invasion and metastasis dependent on the involvement of M2 macrophages. THP-1 cell induction experiment and flow cytometry were performed to explore the effect of IL-33 on macrophage polarization. CCK-8, colony formation, cell apoptosis, cell cycle, cell wound healing and transwell assay were performed to investigate the effect of IL-33 induced M2 macrophages on cell malignant biological behavior by coculturing pancreatic cancer cells with the conditioned medium (CM) from macrophages. We found that miR-548t-5p regulated the expression and secretion of IL-33 in pancreatic cancer cells by directly targeting IL-33 mRNA. IL-33 secreted by cancer cells promoted the recruitment and activation of macrophages to a M2-like phenotype. In turn, IL-33 induced M2 macrophages promoted the migration and invasion of cancer cells. Moreover, IL-33 affected pancreatic cancer cell invasion dependent on the involvement of M2 macrophages in the co-culture system. Thus, our study suggested that manipulation of this IL-33-dependent crosstalk has a therapeutic potential for the treatment of pancreatic cancer metastasis.

Detection of Adverse Event Signals with Severity Grade Classification from Cancer Patient Narrative.

Adverse event (AE) management is crucial to improve anti-cancer treatment outcomes, but it is reported that some AE signals can be missed in clinical visits. Thus, monitoring AE signals seamlessly, including events outside hospitals, would be helpful for early intervention. Here we investigated how to detect AE signals from texts written by cancer patients themselves by developing deep-learning (DL) models to classify posts mentioning AEs according to severity grade, in order to focus on those that might need immediate treatment interventions. Using patient blogs written in Japanese by cancer patients as a data source, we built DL models based on three approaches, BERT, ELECTRA, and T5. Among these models, T5 showed the best F1 scores for both Grade ≥ 1 and ≥ 2 article classification tasks (0.85 and 0.53, respectively). This model might benefit patients by enabling earlier AE signal detection, thereby improving quality of life.

Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.

The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.

T5-like phage BF23 evades host-mediated DNA restriction and methylation.

Bacteriophage BF23 is a close relative of phage T5, a prototypical Tequintavirus that infects Escherichia coli. BF23 was isolated in the middle of the XXth century and was extensively studied as a model object. Like T5, BF23 carries long ∼9.7 kb terminal repeats, injects its genome into infected cell in a two-stage process, and carries multiple specific nicks in its double-stranded genomic DNA. The two phages rely on different host secondary receptors-FhuA (T5) and BtuB (BF23). Only short fragments of the BF23 genome, including the region encoding receptor interacting proteins, have been determined. Here, we report the full genomic sequence of BF23 and describe the protein content of its virion. T5-like phages represent a unique group that resist restriction by most nuclease-based host immunity systems. We show that BF23, like other Tequintavirus phages, resist Types I/II/III restriction-modification host immunity systems if their recognition sites are located outside the terminal repeats. We also demonstrate that the BF23 avoids host-mediated methylation. We propose that inhibition of methylation is a common feature of Tequintavirus and Epseptimavirus genera phages, that is not, however, associated with their antirestriction activity.

TLTC, a T5 exonuclease-mediated low-temperature DNA cloning method.

Molecular cloning is used in a wide variety of biological and medical research. Here, we developed a rapid and efficient DNA-assembling method for routine laboratory work. We discovered that the cleavage speed of T5 exonuclease is approximately 3 nt/min at 0°C and hence developed a T5 exonuclease-mediated low-temperature sequence- and ligation-independent cloning method (TLTC). Two homologous regions of 15 bp-25 bp compatible with the ends of the vector backbones were introduced into the inserts through PCR. Approximately 120 fmol of inserts and linear vectors was mixed at a molar ratio of approximately 3:1 and treated with 0.5 U of T5 exonuclease at 0°C for 5 min. Then, the mixture was transformed into Escherichia coli to generate recombinant plasmids. Single segment and multi-segments can be assembled efficiently using TLTC. For single segment, the overall cloning efficiency is above 95%. Moreover, extra nucleotides in the vectors can be removed during TLTC. In conclusion, an extremely simple and fast DNA cloning/assembling method was established in the present study. This method facilitates routine DNA cloning and synthesis of DNA fragments.

A novel t (5; 17) (q35; q21) associated with t (8; 21) (q22; q22) in a patient with acute myeloid leukemia: case report and review of literature.

The t (8; 21) (q22; q22) with the resulting RUNX1- RUNX1T1 rearrangement is one of the most common cytogenetic abnormalities in acute myeloid leukemia (AML). It is associated with favorable prognosis. The t (5; 17) (q35; q21) is an uncommon translocation, fuses the gene for the nucleophosmin (NPM) to the retinoic acid receptor α(RARA) and was described essentially in acute promyelocytic leukemia (APL) variant. We present the case of a 19-year-old male patient who developed an AML with t (8; 21) (q22; q22) associated to t (5; 17) (q35; 21). Morphology and immunophenotype of the leukemic cells were compatible with AML. The patient received chemotherapy based on cytarabine and anthracycline without all-trans retinoic acid (ATRA) followed by allogenic stem cell transplantation in first remission. To the best of our knowledge, this is the first report of an association between a rare translocation t (5; 17) and t (8; 21) in AML. In this report, we will discuss the prognosis of this association as well as the treatment.

Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil.

Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture.

Acute Undifferentiated Leukemia With a Balanced t(5;10)(q35;p12) Resulting in Fusion of HNRNPH1 With MLLT10.

BACKGROUND/AIM: Acute undifferentiated leukemia (AUL) is leukemia which does not express lineage-specific antigens. Such cases are rare, accounting for 2.7% of all acute leukemia. The reported genetic information of AULs is limited to less than 100 cases with abnormal karyotypes and a few cases carrying chimeric genes or point mutation of a gene. We herein present the genetic findings and clinical features of a case of AUL. CASE REPORT: Bone marrow cells obtained at diagnosis from a 31-year-old patient with AUL were genetically investigated. G-Banding karyotyping revealed an abnormal karyotype: 45,X,-Y,t(5;10)(q35;p12),del(12)(p13)[12]/46,XY[5]. Array comparative genomic hybridization examination confirmed the del(12)(p13) seen by G-banding but also detected additional losses from 1q, 17q, Xp, and Xq corresponding to the deletion of approximately 150 genes from these five chromosome arms. RNA sequencing detected six HNRNPH1::MLLT10 and four MLLT10::HNRNPH1 chimeric transcripts, later confirmed by reverse-transcription polymerase chain reaction together with Sanger sequencing. Fluorescence in situ hybridization analysis showed the presence of HNRNPH1::MLLT10 and MLLT10::HNRNPH1 chimeric genes. CONCLUSION: To the best of our knowledge, this is the first AUL in which a balanced t(5;10)(q35;p12) leading to fusion of HNRNPH1 with MLLT10 has been detected. The relative leukemogenic importance of the chimeras and gene losses cannot be reliably assessed, but both mechanisms were probably important in the development of AUL.

A question-answer generation system for an asynchronous distance learning platform.

Distance learning frees the learning process from spatial constraints. Each mode of distance learning, including synchronous and asynchronous learning, has disadvantages. In synchronous learning, students have network bandwidth and noise concerns, but in asynchronous learning, they have fewer opportunities for engagement, such as asking questions. The difficulties associated with asynchronous learning make it difficult for teachers to determine whether students comprehend the course material. Motivated students will consistently participate in a course and prepare for classroom activities if teachers ask questions and communicate with them during class. As an aid to distance education, we want to automatically generate a sequence of questions based on asynchronous learning content. In this study, we will also generate multiple-choice questions for students to answer and teachers to easily correct. The asynchronous distance teaching-question generation (ADT-QG) model, which includes Sentences-BERT (SBERT) in the model architecture to generate questions from sentences with a higher degree of similarity, is proposed in this work. With the Wiki corpus generation option, it is anticipated that the Transfer Text-to-Text Transformer (T5) model will generate more fluent questions and be more aligned with the instructional topic. The results indicate that the questions created by the ADT-QG model suggested in this work have good fluency and clarity indicators, showing that the questions generated by the ADT-QG model are of a certain quality and relevant to the curriculum.

Disynaptic inhibition shapes tuning of OFF-motion detectors in Drosophila.

The circuitry underlying the detection of visual motion in Drosophila melanogaster is one of the best studied networks in neuroscience. Lately, electron microscopy reconstructions, algorithmic models, and functional studies have proposed a common motif for the cellular circuitry of an elementary motion detector based on both supralinear enhancement for preferred direction and sublinear suppression for null-direction motion. In T5 cells, however, all columnar input neurons (Tm1, Tm2, Tm4, and Tm9) are excitatory. So, how is null-direction suppression realized there? Using two-photon calcium imaging in combination with thermogenetics, optogenetics, apoptotics, and pharmacology, we discovered that it is via CT1, the GABAergic large-field amacrine cell, where the different processes have previously been shown to act in an electrically isolated way. Within each column, CT1 receives excitatory input from Tm9 and Tm1 and provides the sign-inverted, now inhibitory input signal onto T5. Ablating CT1 or knocking down GABA-receptor subunit Rdl significantly broadened the directional tuning of T5 cells. It thus appears that the signal of Tm1 and Tm9 is used both as an excitatory input for preferred direction enhancement and, through a sign inversion within the Tm1/Tm9-CT1 microcircuit, as an inhibitory input for null-direction suppression.

Biomedical Relation Extraction Using Dependency Graph and Decoder-Enhanced Transformer Model.

The identification of drug-drug and chemical-protein interactions is essential for understanding unpredictable changes in the pharmacological effects of drugs and mechanisms of diseases and developing therapeutic drugs. In this study, we extract drug-related interactions from the DDI (Drug-Drug Interaction) Extraction-2013 Shared Task dataset and the BioCreative ChemProt (Chemical-Protein) dataset using various transfer transformers. We propose BERTGAT that uses a graph attention network (GAT) to take into account the local structure of sentences and embedding features of nodes under the self-attention scheme and investigate whether incorporating syntactic structure can help relation extraction. In addition, we suggest T5slim_dec, which adapts the autoregressive generation task of the T5 (text-to-text transfer transformer) to the relation classification problem by removing the self-attention layer in the decoder block. Furthermore, we evaluated the potential of biomedical relation extraction of GPT-3 (Generative Pre-trained Transformer) using GPT-3 variant models. As a result, T5slim_dec, which is a model with a tailored decoder designed for classification problems within the T5 architecture, demonstrated very promising performances for both tasks. We achieved an accuracy of 91.15% in the DDI dataset and an accuracy of 94.29% for the CPR (Chemical-Protein Relation) class group in ChemProt dataset. However, BERTGAT did not show a significant performance improvement in the aspect of relation extraction. We demonstrated that transformer-based approaches focused only on relationships between words are implicitly eligible to understand language well without additional knowledge such as structural information.

Anxiety in Brief: Assessment of the Five-Item Trait Scale of the State-Trait Anxiety Inventory in South Africa.

The current study examined the psychometric properties of a short form of the trait scale of the Spielberger State-Trait Anxiety Inventory. Participants consisted of a convenience sample of students (n = 322) who completed the five-item version of the trait scale of the State-Trait Anxiety Inventory, the Perceived Stress Scale, the nine-item version of the Beck Hopelessness Scale, the 10-item version of the Center for Epidemiological Studies Depression Scale, and the Post-Traumatic Stress Disorder Checklist. We used classical test theory and item response theory (Rasch and Mokken analyses) to examine the psychometric properties of a previously proposed five-item version of this scale. These approaches confirmed that the five-item measure of anxiety had satisfactory reliability and validity, and also confirmed that the five items comprised a unidimensional scale.

Sequence-to-sequence pretraining for a less-resourced Slovenian language.

Introduction: Large pretrained language models have recently conquered the area of natural language processing. As an alternative to predominant masked language modeling introduced in BERT, the T5 model has introduced a more general training objective, namely sequence to sequence transformation, which more naturally fits text generation tasks. The monolingual variants of T5 models have been limited to well-resourced languages, while the massively multilingual T5 model supports 101 languages. Methods: We trained two different-sized T5-type sequence-to-sequence models for morphologically rich Slovene language with much fewer resources. We analyzed the behavior of new models on 11 tasks, eight classification ones (named entity recognition, sentiment classification, lemmatization, two question answering tasks, two natural language inference tasks, and a coreference resolution task), and three text generation tasks (text simplification and two summarization tasks on different datasets). We compared the new SloT5 models with the multilingual mT5 model, multilingual mBART-50 model, and with four encoder BERT-like models: multilingual BERT, multilingual XLM-RoBERTa, trilingual Croatian-Slovene-English BERT, and monolingual Slovene RoBERTa model. Results: Concerning the classification tasks, the SloT5 models mostly lag behind the monolingual Slovene SloBERTa model. However, these models are helpful for generative tasks and provide several useful results. In general, the size of models matters, and currently, there is not enough training data for Slovene for successful pretraining of large models. Discussion: While the results are obtained on Slovene, we believe that they may generalize to other less-resourced languages, where such models will be built. We make the training and evaluation code, as well as the trained models, publicly available.

Phylogenetic distribution, structural analysis and interaction of nucleotide excision repair proteins in cyanobacteria.

Cyanobacteria are photosynthetic Gram-negative, oxygen evolving prokaryotes with cosmopolitan distribution. Ultraviolet radiation (UVR) and other abiotic stresses result in DNA lesions in cyanobacteria. Nucleotide excision repair (NER) pathway removes the DNA lesions produced by UVR to normal DNA sequence. In cyanobacteria, detailed knowledge about NER proteins is poorly studied. Therefore, we have studied the NER proteins in cyanobacteria. Analyses of 289 amino acids sequence from 77 cyanobacterial species have revealed the presence of a minimum of one copy of NER protein in their genome. Phylogenetic analysis of NER protein shows that UvrD has maximal rate of amino acid substitutions which resulted in increased branch length. The motif analysis shows that UvrABC proteins is more conserved than UvrD, Further, UvrA with UvrB protein interacts with each other and form stable complex which have DNA binding domain on the surface of the complex. UvrB also have DNA binding domain. Positive electrostatic potential was found in the DNA binding region, which is followed by negative and neutral electrostatic potential. Additionally, the surface accessibility values at the DNA strands of T5-T6 dimer binding site were maximal. Protein nucleotide interaction shows the strong binding of T5-T6 dimer with NER proteins of Synechocystis sp. PCC 6803. This process repairs the UV-induced DNA lesions in dark when photoreactivation is inactive. Regulation of NER proteins protect cyanobacterial genome and maintain the fitness of organism under different abiotic stresses.

Broad-host-range lytic Erwinia phage Key with exopolysaccharide degrading activity.

In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key phage has a 115,651 bp long double-stranded DNA genome with the G + C ratio of 39.03%, encoding 182 proteins and 27 tRNA genes. The majority (69%) of predicted coding sequences (CDSs) encode proteins with unknown functions. The protein products of 57 annotated genes were found to have probable functions in nucleotide metabolism, DNA replication, recombination, repair, and packaging, virion morphogenesis, phage-host interaction and lysis. Furthermore, the product of gene 141 shared amino acid sequence similarity and conserved domain architecture with the exopolysaccharide (EPS) degrading proteins of Erwinia and Pantoea infecting phages as well as bacterial EPS biosynthesis proteins. Due to the genome synteny and similarity to the proteins of T5-related phages, phage Key, together with its closest relative, Pantoea phage AAS21, was suggested to represent a novel genus within the Demerecviridae family, for which we tentatively propose the name "Keyvirus".