Complete Sequence Research Articles

Analysis of bZIP transcription factors in Rhododendron simsii and functional study of RsbZIP6 in regulating anthocyanin biosynthesis

The basic leucine zipper (bZIP) transcription factors play a critical role in various plant biological processes, including anthocyanin biosynthesis. This study focuses on Rhododendron simsii, a notable ornamental species with insufficiently explored bZIP transcription factors. We identified 66 bZIP transcription factors in the R. simsii genome and conducted comprehensive bioinformatics analyses to determine their gene localization, phylogenetic relationships, grouping, gene/protein structure, duplication events, synteny, and expression profiles. Our analysis identified RsbZIP6, a homolog of HY5 known to influence anthocyanin biosynthesis in many plants, as a potential regulator of this pathway. We cloned the complete coding sequence of RsbZIP6, which encodes a 170-amino acid protein spanning 510 bp. Subcellular localization analysis verified the nuclear presence of the RsbZIP6 protein. RT-qPCR analysis revealed the highest expression of RsbZIP6 in petals, which correlated with anthocyanin accumulation. Transgenic experiments indicated that overexpressing RsbZIP6 in Arabidopsis enhanced anthocyanin accumulation by upregulating genes involved in anthocyanin biosynthesis (4CL, CHS, CHI, DFR, F3H, F3’H, ANS and UF3GT). Our findings enhance understanding of the bZIP transcription factor family in R. simsii and underscore the vital role of RsbZIP6 in anthocyanin biosynthesis, providing insights for future genetic enhancement strategies.

Complete genome sequence of Promicromonospora sp. strain Populi, an actinobacterium isolated from Populus trichocarpa rhizosphere.

Promicromonospora sp. strain Populi is an actinobacterium isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa. We completely sequenced its 5.2-Mbp chromosome using Oxford Nanopore long reads and predicted it to encode 4,685 proteins, 3 rRNA operons, and 54 tRNAs and noncoding RNAs.

Plastid phylogenomics of Robinsonia (Senecioneae; Asteraceae), endemic to the Juan Fernández Islands: insights into structural organization and molecular evolution

BackgroundThe genus Robinsonia DC. (tribe Senecioneae, Asteraceae) endemic to the Juan Fernández Islands in Chile is one of the most conspicuous insular plant groups in the world. Unlike typical herbaceous Asteraceae plants, these plants demonstrate spectacular and unusual rosette tree growth forms as shown by the alpine giant senecios (genus Dendrosenecio, tribe Senecioneae) endemic to the East African mountains. However, monophyly of the genus and phylogenetic relationships among species of Robinsonia as well as their plastome evolution remain elusive. This study aims to explore their phylogeny, species diversification, and molecular evolution based on the complete plastome sequences in the context of adaptive radiation on oceanic islands.ResultsThe insular Robinsonia plastomes are highly conserved in their structures and organization of contents. Five divergence hotspots as potential chloroplast markers and five positively selected coding genes (accD, ndhF, rpoA, ycf1, and ycf2) are identified. Robinsonia plastomes has an overall nucleotide diversity higher than that of the sky island Dendrosenecio, but much lower than herbaceous Senecio. Phylogenetic analysis demonstrates the monophyly of Robinsonia and identifies two major infrageneric lineages. Both Robinsonia and Dendrosenecio are deeply nested within large genus Senecio.ConclusionsWhile plastid genomes of Robinsonia are highly conserved, their sequences strongly demonstrated the monophyly of the genus and inferred robust interspecific relationships, including herbaceous Senecio and woody Dendrosenecio. Different sets of positively selected chloroplast genes, five for Robinsonia and two for Dendrosenecio, may play an important role in the adaptation strategies of these fascinating woody species in insular and continental sky island habitats. Overall phylogenetic positions and sister lineages of Robinsonia and Dendrosenecio require additional study based on broader sampling of Senecio.

Numerical simulation on multi-well fracturing considering multiple thin layers in vertical direction

Multiwell fracturing is a key technology for developing shale gas and shale oil reservoirs. In this study, a multiple planar 3D (PL3D) fracture simulator that can capture multiple thin layers was developed to examine the propagation of multiple fractures during multicluster fracturing in multiple horizontal wells. The simulator considers multiple thin layers in the vertical direction. The results of the model are validated against the analytical solution of a single radial fracture and the implicit level set algorithm (ILSA). Using the simulator, a series of numerical simulations based on the field case are performed to investigate the fracture propagation mechanism of multiwell fracturing. The completion sequence, well placement pattern, well spacing, and cluster spacing are investigated to optimize the treatment parameters. The effective fracture area is used to quantitatively describe the stimulation effect. The adaptability of the completion sequence and well placement pattern is also analysed from the perspective of “frac hits”. The results show that the completion sequence has a critical influence on the stimulation effect and fracture geometry. From the perspective of avoiding “frac-hit” fractures, fracturing the low-stress layer can form an “artificial stress barrier”, which slightly protects the well from interference from other fractures. The staggered well pattern is better than the stacked well pattern. Compared with the stacked pattern, the staggered pattern can reduce the overlap area of fractures by 80 %, which greatly reduces the probability of “frac-hits”. With increasing well spacing from 200 m to 500 m, the fracture area increases by 25 %, and the degree of uneven stimulation between the two pay zones also increases by 6 %. Considering that a small well spacing is prone to “frac hits”, a large well spacing leads to an unstimulated area between two wells, and a 350 m well spacing is optimal. The effective fracture area decreases slightly with increasing perforation cluster spacing, but the fracture geometry becomes much more regular. The results can be helpful for the field design of multiwell fracturing.

Deep‐Learning‐Based Facial Retargeting Using Local Patches

AbstractIn the era of digital animation, the quest to produce lifelike facial animations for virtual characters has led to the development of various retargeting methods. While the retargeting facial motion between models of similar shapes has been very successful, challenges arise when the retargeting is performed on stylized or exaggerated 3D characters that deviate significantly from human facial structures. In this scenario, it is important to consider the target character's facial structure and possible range of motion to preserve the semantics assumed by the original facial motions after the retargeting. To achieve this, we propose a local patch‐based retargeting method that transfers facial animations captured in a source performance video to a target stylized 3D character. Our method consists of three modules. The Automatic Patch Extraction Module extracts local patches from the source video frame. These patches are processed through the Reenactment Module to generate correspondingly re‐enacted target local patches. The Weight Estimation Module calculates the animation parameters for the target character at every frame for the creation of a complete facial animation sequence. Extensive experiments demonstrate that our method can successfully transfer the semantic meaning of source facial expressions to stylized characters with considerable variations in facial feature proportion.

Surveillance for Avian Influenza in Wild Birds in the Lombardy Region (Italy) in the Period 2022–2024

Influenza A virus (AIV) circulation was investigated in the Lombardy region, during 2022–2024, in wild ducks (through hunting and sampling of faecal samples within natural parks) and wild birds found dead. Samples were analysed through real-time RT-PCRs for Influenza A virus, H5 and H7. Whole genome sequencing was performed on AIV-positive samples. Screening of 3497 hunted Anatidae revealed a total of 184 positive samples. Complete sequencing of 136 samples highlighted the presence of 21 different subtypes ranging from H1N1 to H12N5. The H5N1 HPAIV (high pathogenic AIV) subtype, clade 2.3.4.4b, was the most common during the 2022–2023 winter season (31.8%), while H5 LPAI (low pathogenic AIV) strains were the most prevalent (28.6%) in the 2023–2024 season. The molecular survey on wild birds found dead (n = 481) showed two positive buzzards (14%, 2/14), one grey heron (5.5%, 1/18) and one kestrel (7.6%, 1/13). Regarding the order of Charadriiformes, the dead gulls sampled in 2022 (17 birds) were all negative, whereas 85 out of 167 (51%) individuals were positive in 2023. All positives were caused by an H5N1 HPAIV clade 2.3.4.4b virus belonging to genotype BB. All the faecal samples (1699) received from passive surveillance in nature parks were analysed for AIV with negative results.

Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms. For complete genome nucleotide sequences, BSMYV-IN4 and IN5 shared 77-79% identity with other BSMYVs, while BSMYV-IN7 and IN8 exhibited identities of 77-97%. This study reports for the first time, the complete genomes of two banana streak IM virus (BSIMV-IN1 and -IN2) infecting triploid banana hybrids exhibiting leaf distortion, stunted rosette-like growth, and necrosis, sharing 87% sequence identity with reference BSIMV genome (GenBank accession no. HQ593112). Phylogenetic inference based on complete genomes revealed the distinct and congruent placement of BSMYV-IN4 and IN5 within the BSMYV cluster. Pairwise sequence comparisons of the conserved RT/RNase H nucleotide (nt) sequences revealed that the BSMYV-IN7 and IN4 isolates showed 85% and 97% identity to BSMYV (AY805074), respectively, which shared highest nt identity with BSMYV-IN6, IN9, and IN10, at 100%. The RT/RNase H nt sequences of BSIMV-IN1 and IN2 had 98% identity with the BSIMV (HQ593112), but were characterized as novel variants of BSIMV based on complete genomes. An analysis of relative synonymous codon usage (RSCU) pattern in the ORFIII polyprotein of BSMYV and BSIMV isolates revealed AGA and AGG (arginine) as the most frequently overrepresented codons (>1.5), evolutionary conserved in the genome of both species. A total of 14 recombination events were detected among the 36 BSV genomes, with recombination breakpoints mainly located in the ORFI, III, and IGR genomic regions. A novel phylogenetic cluster, comprised of BSMYV-IN4 and IN5 within the clade I was probably derived from heterologous recombination between parents resembling banana streak VN virus (BSVNV; AY750155) and banana streak GF virus (BSGFV; KJ013507) isolates. The present study conclusively reports the infection of genetically and symptomatically distinct variants of BSMYV and BSIMV infecting banana hybrids in NER India.

Generative AI Models for the Protein Scaffold Filling Problem.

De novo protein sequencing is an important problem in proteomics, playing a crucial role in understanding protein functions, drug discovery, design and evolutionary studies, etc. Top-down and bottom-up tandem mass spectrometry are popular approaches used in the field of mass spectrometry to analyze and sequence proteins. However, these approaches often produce incomplete protein sequences with gaps, namely scaffolds. The protein scaffold filling problem refers to filling the missing amino acids in the gaps of a scaffold to infer the complete protein sequence. In this article, we tackle the protein scaffold filling problem based on generative AI techniques, such as convolutional denoising autoencoder, transformer, and generative pretrained transformer (GPT) models, to complete the protein sequences and compare our results with recently developed convolutional long short-term memory-based sequence model. We evaluate the model performance both on a real dataset and generated datasets. All proposed models show outstanding prediction accuracy. Notably, the GPT-2 model achieves 100% gap-filling accuracy and 100% full sequence accuracy on the MabCampth protein scaffold, which outperforms the other models.

Novel Porcine Getah Virus from Diarrheal Piglets in Jiangxi Province, China: Prevalence, Genome Sequence, and Pathogenicity.

Getah virus (GETV) is a mosquito-borne virus belonging to the genus Alphavirus in the family Togaviridae. Its infection poses an increasing threat to animals and public health in China. In this study, an epidemiological survey of GETV on 46 pig farms in Jiangxi Province, China, was performed; GETV isolation and characterization were carried out, including a complete sequence determination and phylogenetic analysis; and pathogenicity of the GETV was experimentally investigated by inoculating newborn piglets with the isolated GETV strain. Epidemiological studies conducted on the organs of infected pigs, aborted piglets, and the blood of aborted sows sampled from pig farms in Jiangxi Province, China, demonstrated that 44 out of the 46 pig farms were positive for GETV, which is a positivity rate of 95.65% (44/46). Of the 411 samples tested, 47.93% (197/411) were found positive for GETV. A GETV strain called GETV-JX-CHN-22 was obtained, which showed stable proliferation in Vero cells. One-step growth curve results showed that the GETV-JX-CHN-22-P7 (passage 7) isolate reached a peak titer of 108.3 TCID50/mL at 24 hpi. An analysis of the whole-genome sequencing results showed that GETV-JX-CHN-22 (prototype) and GETV-JX-CHN-22-P7 shared nucleotide sequence similarities of 95.3% to 99.6% with 73 reference strains of GETV in GenBank. Genetic evolution analysis revealed that GETV-JX-CHN-22 and GETV-JX-CHN-22-P7 belonged to the GIII group, the same group members of most strains were reported in China. Animal inoculation experiments indicated that piglets exhibited typical symptoms and pathological changes of GETV infection after 24 h inoculation, which reproduced the pathogenicity of GETV field strain infections in piglets. To our knowledge, this study is the first report on the detection and isolation of porcine GETV associated with diarrhea from pig farms in Jiangxi Province, China. It is of great importance to study the infection spectrum, transmission mechanism, and public health significance of GETV. The results provide foundations for the genomic and biological (pathogenic) characteristics of the circulating GETV in Jiangxi Province, China.

Case Report: Hemoglobin Hasharon with Concurrent Alpha Thalassemia in a Patient with Maple Syrup Urine Disease

Abstract Hemoglobin Hasharon (Hb Hasharon) is an unstable hemoglobin variant stemming from a mutation in the alpha globin gene. This mutation involves the replacement of aspartic acid with histidine at position 47 of the alpha globin chain. Initially identified in 1967 in Israel, Hb Hasharon has since been sporadically reported in various populations, including in Italy, Greece, Germany, and among Latin Americans of Mediterranean descent. Only three English articles have reported several cases of the combined alpha thalassemia deletion and Hasharon mutation, all between 1978-1980. Notably, there has been no prior report of Hb Hasharon with concurrent alpha thalassemia in patients with maple syrup urine disease (MSUD). We hereby present the first case of Hb Hasharon with alpha thalassemia in a patient diagnosed with MSUD. This patient, a 16-month-old female, received a prenatal diagnosis of MSUD through amniocentesis, confirming homozygosity for a known pathogenic variant in DBT (c.75_76delAT, p.C26wfsX2). Prompt initiation of formula feeding has effectively controlled her MSUD. The patient was referred for further evaluation due to hemoglobin newborn screen showing hemoglobin A, Hb F and “variant hemoglobin”. Her parents denied any family history of hemoglobinopathy. Her complete blood count was predominantly normal except for mild microcytosis, with a mean corpuscular volume of 69.1 fl (normal range 70.0-86.0 fl). The patient didn’t exhibit neonatal jaundice or any other signs or symptoms of hemolysis. The reticulocyte count was also within normal limits. The hemoglobin electrophoresis results revealed a complex pattern, with 28.8% of an unknown hemoglobin between zone 4 and 5 on capillary zone electrophoresis (CZE) as well as a possible A2 variant in zone 1. High-performance liquid chromatography (HPLC) indicated a 29.1% peak at a retention time of 4.72 minutes, along with several smaller peaks, that were indicative of the degradation of the unstable unknown hemoglobin. Although the zones and retention time aligned with Hb Hasharon, the percentage differed from the expected range of 19-20% in CZE and 18-21% in HPLC for this variant, prompting the team to order alpha and beta globin sequencing tests. Beta globin gene complete sequencing yielded negative results, while the sequencing of alpha globin gene revealed that the patient carries one copy of the -alpha3.7 alpha-globin deletion and one copy of the c.142G>C (p.Asp48His) variant in the alpha2-globin (HBA2) gene, resulting in an -alpha/alpha2alpha1 genotype with Hb Hasharon. While Hb Hasharon is generally not clinically significant, its co-occurrence with alpha-thalassemia can lead to hemolytic anemia. In our patient, clinic and chemical parameters were predominantly within normal ranges, except for mild microcytosis. The potential interaction between MSUD and Hb Hasharon with concurrent alpha thalassemia remains unknown. Continued patient monitoring will enable us to evaluate whether these conditions may influence each other’s clinical and biochemical profiles.

Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome

BackgroundMicrosatellites are increasingly realized to have biological significance in human genome and health in past decades, the assembled complete reference sequence of human genome T2T-CHM13 brought great help for a comprehensive study of short tandem repeats in the human genome.ResultsMicrosatellites density landscapes of all 24 chromosomes were built here for the first complete reference sequence of human genome T2T-CHM13. These landscapes showed that short tandem repeats (STRs) are prone to aggregate characteristically to form a large number of STRs density peaks. We classified 8,823 High Microsatellites Density Peaks (HMDPs), 35,257 Middle Microsatellites Density Peaks (MMDPs) and 199, 649 Low Microsatellites Density Peaks (LMDPs) on the 24 chromosomes; and also classified the motif types of every microsatellites density peak. These STRs density aggregation peaks are mainly composing of a single motif, and AT is the most dominant motif, followed by AATGG and CCATT motifs. And 514 genomic regions were characterized by microsatellite density feature in the full T2T-CHM13 genome.ConclusionsThese landscape maps exhibited that microsatellites aggregate in many genomic positions to form a large number of microsatellite density peaks with composing of mainly single motif type in the complete reference genome, indicating that the local microsatellites density varies enormously along the every chromosome of T2T-CHM13.

The complete mitochondrial genome of the endangered Atlantic Pygmy Devil Ray, Mobula hypostoma (Bancroft, 1831), from Brazil.

Mobulidae is a monophyletic family within the Myliobatiformes that comprises pelagic species represented by manta and devil rays. Among the genus Mobula, the Atlantic Pygmy Devil Ray - Mobula hypostoma - is reported in coastal regions exclusively in tropical and subtropical Atlantic Ocean from 1 to 100m deep. In Brazil, M. hypostoma is one of the least studied Mobula species. It is regularly misidentified, especially as Mobula thurstoni, and is commonly listed as bycatch, in fishery inventories, or related to opportunistic sightings in the national territory. Here, we describe the complete nucleotide sequence of the mitochondrial genome (mitogenome) from Mobula hypostoma, which is 18,141bp in length and comprises 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The M. hypostoma mitochondrial genes organisation and mitochondrial genome length are similar to other Mobula species, and the phylogenetic reconstruction indicates M. hypostoma as closely related to Mobula munkiana. The Brazilian mitogenome of M. hypostoma is expected to be a valuable resource for molecular-based species identification, and evolutionary and phylogeography studies.

Structural characterization of wild edible Pleurotuscollected from Punjab, India

Oyster mushroom (Pleurotus spp.) belongs to the class Basidiomycetes, family Agaricaceae, commonly known as ‘dhingri’ in India and proliferates naturally on dead, decay wooden logs or trunks of deciduous or coniferous woods in tropical and temperate forests. Although Pleurotus mushrooms are commercially important mushrooms but wild Pleurotus still require public recognition. Hence, the present study aimed to conduct a field survey for collection of Pleurotus mushrooms from wild regions of of Punjab Two wild Pleurotus were collected and domesticated at Mushroom Research Complex, Punjab Agricultural University, Ludhiana, Punjab which were further analyzed at molecular and biochemical levels. These mushrooms were identified at species level through ITS (Internal transcribed spacer region) based method (18S ribosomal RNA gene, internal transcribed spacer, 5.8S ribosomal RNA gene, complete sequence; and 28S ribosomal RNA gene) was carried out. The gene bank accessioned Pleurotus sapidus as MK 281339 and Pleurotus floridanus as MK 281340. Hyphae of Pleurotus sapidus was observed to be packed tightly to a greater extent as compared to Pleurotus floridanus according to the ultra-structure recorded by scanning electron microscope. Both species of Pleurotus share two different proteins of same molecular weight 24.81 KDa and 28.43 KDa. Collecting and identifying wild species is crucial to preserve the wild fruits and fathom out the benefits of wild edible Pleurotus spp.

A Novel Trichinella spiralis Galectin Strengthens the Macrophage ADCC Killing of Larvae via Driving M1 Polarization.

Galectin recognizes β-galactosides through its carbohydrate recognition domains (CRDs). This study aimed to determine the biological features of a novel Trichinella spiralis galectin (galactoside-binding lectin family protein, TsGLFP) and its role in driving macrophage M1 polarization and enhancing ADCC killing of larvae. TsGLFP belongs to the galectin family and has two CRDs. The complete TsGLFP cDNA sequence was cloned and then expressed in Escherichia coli BL21. The results of qPCR, Western blot, and indirect immunofluorescence tests (IIFTs) revealed that TsGLFP was expressed in various stages of T. spiralis worms and principally localized at the cuticle and around the female embryos of the nematode. rTsGLFP had the function of agglutinating mouse erythrocytes, and this agglutination activity could be inhibited by lactose. After the mouse macrophage RAW264.7 was incubated with rTsGLFP, the expression level of the M1 genes (iNOS, IL-6, and TNF-α) and NO production were obviously increased. After incubating macrophages with rTsGLFP, there was a noticeable rise in the expression levels of p-IκB-α and p-NF-κB p65. Additionally, rTsGLFP enhanced the macrophage's ability to kill newborn larvae by ADCC cytotoxicity. When the macrophages were pretreated with the specific p-NF-κB p65 inhibitor PDTC, and then stimulated with rTsGLFP, the expression levels of iNOS, NO, and p-NF-κB p65 and the macrophages' ADCC cytotoxicity were distinctly decreased. These findings indicated that rTsGLFP enhanced the macrophage ADCC killing of larvae by driving M1 polarization through activating the NF-κB pathway.

Identification, Purification, and Characterization of Kunitz-Type Protease Inhibitors from White-Fleshed Dragon Fruit (Selenicereus undatus) and Red-Fleshed Dragon Fruit (Selenicereus costaricensis) Seeds as Novel Food Allergens.

There have been clinical reports of allergies to dragon fruits. However, little is known about the allergens that trigger these reactions. This study aimed to investigate novel allergens in dragon fruits. The peptide mass fingerprints of two purified natural allergens were identified by LC-MS/MS with chymotrypsin proteolysis. The complete amino acid sequences of the allergens were deduced from cDNA amplicon sequences. The coding sequences of two allergens were inserted in the expression vector pColdI, and recombinant allergens were produced in Escherichia coli. Circular dichroism was performed to analyze the secondary structures of natural and recombinant allergens. Our results identified two novel allergens as Kunitz-type protease inhibitors. Recombinant allergens exhibited well-folded structures, predominantly composed of β-sheets, similar to their natural counterparts. IgE reactivity analysis with sera from ten patients primarily sensitized to dragon fruit indicated that Kunitz-type protease inhibitors are major allergens in dragon fruits. These results improve our understanding of allergen sources and provide important insights into the allergenicity of proteins from different species.

Complete sequencing of ape genomes.

We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.

Complete genome sequence of the avian paramyxovirus serotype 9 strain duck/Miyazaki/128/2021.

Here, we report the complete genome sequence of the avian paramyxovirus serotype 9 strain duck/Miyazaki/128/2021, which was determined using the Illumina MiSeq platform. The position of the hemagglutinin-neuraminidase stop codon differed from that of the only other available completely sequenced prototype strain, duck/New York/22/1977.

NADPH-cytochrome P450 reductase involved in the lambda-cyhalothrin susceptibility on the green mirid bug Apolygus lucorum.

NADPH-cytochrome P450 reductase (CPR) is crucial for the detoxification process catalysed by cytochrome P450, which targets various exogenous xenobiotics, as well as pesticides. In our research, we successfully obtained the complete cDNA sequence of Apolygus lucorum's CPR (AlCPR) using reverse transcription PCR along with rapid amplification of cDNA ends technology. Bioinformatics analysis exhibited that the inferred amino acid sequence of AlCPR is characteristic of standard CPRs, featuring an N-terminal membrane anchor and three conserved FMN, FAD and NADP binding sites. Phylogenetic result revealed that AlCPR was positioned within the Hemiptera cluster, showing a close evolutionary relationship with the CPR of Cimex lectularius. The real-time quantitative PCR results demonstrated widespread expression of AlCPR across various life stages and tissues of A. lucorum, with the most prominent expression in adults and the abdominal region. Injecting double-stranded RNA of AlCPR only significantly increased the lambda-cyhalothrin susceptibility in lambda-cyhalothrin-resistant strain rather than the susceptible strain. These findings suggest a potential link between AlCPR and the P450-dependent defence mechanism against lambda-cyhalothrin in A. lucorum.

Structural and functional characterization of haemoglobin genes in Labeo catla: Insights into hypoxic adaptation and survival

Haemoglobin (HB) protein comprises four subunits: two identical α-subunits (HBA) and two identical β-subunits (HBB), encoded by the HBA and HBB genes. In this investigation, 5′/3′ RACE PCR (Rapid Amplification of cDNA Ends) was used to obtain complete coding sequences (CDSs) of both the genes from farmed Labeo catla. The resulting CDSs were 432 base pairs and 447 base pairs for HBA and HBB, respectively, corresponding to 143 and 148 amino acids. Phylogenetic analysis revealed close relationships with other cyprinids, with Labeo rohita being the closest relative. Functional analysis and protein structure prediction were conducted using bioinformatics tools. Expression profiling of both genes was checked in various tissues under control (C) and hypoxic (H) conditions. Notably, under hypoxia, HBA and HBB genes were significantly upregulated (P < 0.05) initially, followed by a return to normal expression levels. Similar trends were observed for Hif1α (Hypoxia-inducible factor one alpha) and EPO (Erythropoietin) genes. Additionally, haematological indices also significantly increased corresponding to the gene expressions. However, with the decrease in the expression of these genes an onset of mortality was observed in the hypoxia (H) treated groups. The results of the current study explored the role of haemoglobin genes in adaptation to the hypoxic condition.

B-246 Pab to mab conversion via mass spectrometry: direct antibody discovery from serum

Abstract Background Navigating the intricacies of discovering unique and functional antibody binders for in vitro diagnostic development comes with several technological challenges, such as limited diversity of antibody repertoires, functional screening challenges, and the absence of suitable in vitro models. A proteomics-driven strategy to antibody discovery is a promising solution to overcome these obstacles by facilitating polyclonal to monoclonal antibody conversion. De novo polyclonal antibody sequencing utilizes mass spectrometry and machine-learning driven bioinformatics to obtain complete antibody sequences from immunoserum or purified protein samples. This approach investigates the entire circulating antibody repertoire at the protein level, thereby broadening the spectrum of potential candidates. It further facilitates functional selection by enabling antibody purification and enrichment techniques. This capability facilitates the identification of antibodies possessing unique functions, crucial for subsequent downstream development. We demonstrate the application and de novo polyclonal antibody sequencing using mass spectrometry and machine learning bioinformatics to enable the next generation of antibody discovery. Methods In this study, we employed a novel mass spectrometry-based approach, REpAb, to de novo sequence polyclonal antibodies directly from the immunized serum of animals or human patients. REpAb integrates mass spectrometry with machine learning-based bioinformatics to de novo sequence and assemble monoclonal antibodies from a polyclonal mixture. Protein lysates underwent analysis using an Orbitrap EclipseTM Series instrument (ThermoFisher Scientific, CA, US) coupled with the LC Evosep One (Evosep, Denmark). Results De novo polyclonal sequencing with REpAb yielded unique antibody binders not found in splenocytes or peripheral blood mononuclear cells (PBMCs). De novo antibody sequencing-discovered antibody sequences from naturally exposed humans showed unrestricted germline usage, compared to restricted germline used in antigen-immunized animals. Additionally, a proteomics-based approach for antibody discovery enables functional antibody selection through standard protein A/G purification, followed by negative and positive selection enrichment strategies to isolate antibody clones specific to the region of interest on the antigen. Conclusions Sequencing antibodies at the protein level directly reflects the circulating antibody repertoires, which expands the antibody diversity from the BCR repertoire. Proteomic-based antibody discovery empowers the functional selection of antibodies via meticulously designed enrichment strategies. This approach allows for the identification of a diverse pool of candidates possessing specific functions, such as anti-idiotypic features.