Comprehensive insights into AML relapse: genetic mutations, clonal evolution, and clinical outcomes.

INTRODUCTION: Acute myeloid leukemia (AML) is a complex hematologic malignancy characterized by uncontrolled proliferation of myeloid precursor cells within bone marrow. Despite advances in understanding of its molecular underpinnings, AML remains a therapeutic challenge due to its high relapse rate and clonal evolution. METHODS: In this retrospective study, we analyzed data from 24 AML patients diagnosed at a single institution between January 2017 and August 2023. Comprehensive genetic analyses, including chromosomal karyotyping, next-generation sequencing, and gene fusion assays, were performed on bone marrow samples obtained at initial diagnosis and relapse. Clinical data, treatment regimens, and patient outcomes were also documented. RESULTS: Mutations in core genes of FLT3, NPM1, DNMT3A, and IDH2 were frequently discovered in diagnostic sample and remained in relapse sample. FLT3-ITD, TP53, KIT, RUNX1, and WT1 mutation were acquired at relapse in one patient each. Gene fusion assays revealed stable patterns, while chromosomal karyotype analyses indicated a greater diversity of mutations in relapsed patients. Clonal evolution patterns varied, with some cases showing linear or branching evolution and others exhibiting no substantial change in core mutations between diagnosis and relapse. CONCLUSIONS: Our study integrates karyotype, gene rearrangements, and gene mutation results to provide a further understanding of AML heterogeneity and evolution. We demonstrate the clinical relevance of specific mutations and clonal evolution patterns, emphasizing the need for personalized therapies and measurable residual disease monitoring in AML management. By bridging the gap between genetics and clinical outcome, we move closer to tailored AML therapies and improved patient prognoses.

Evaluation of a 3D-Printed Reduction Guide for Minimally Invasive Plate Osteosynthesis of Short Oblique Radial Diaphyseal Fracture in Dogs: A Cadaveric Study.

This study aims to evaluate the clinical application of three-dimensional (3D)-printed custom reduction guides (3DRG) for minimally invasive plate osteosynthesis (MIPO) of short oblique radial diaphyseal fractures. Canine forelimb specimens (n = 24) were prepared and a diaphyseal short oblique fracture was simulated in the distal radius and ulna. Bone fragments were stabilized with the MIPO technique using a 3DRG (Group A), open reduction (Group B), or closed reduction with circular external skeletal fixation (ESF) (Group C). The diaphyseal short oblique fractures were created in each radius at one-third of the radial length from the distal radial articular surface. Surgical stabilization of the fractures was performed in each group. Pre and postoperative radiographic images were obtained to measure frontal angulation (FA), sagittal angulation (SA), frontal joint reference line angulation (fJRLA), sagittal joint reference line angulation (sJRLA), translational malalignment and fracture gap width. Surgical time was also measured. In the homogeneity test, differences in SA, sJRLA, craniocaudal translation and fracture gap before and after surgery had no significant difference among the three groups. On the other hand, differences in FA, fJRLA, mediolateral translation and surgical time before and after surgery had significant differences among the three groups. In the post hoc test, only surgical time showed a significant difference between the three groups, and group A showed the shortest surgical time. The use of 3DRG for MIPO of short oblique radial diaphyseal fractures in dogs is reliable for the alignment and apposition of fractures and reduces surgical time.

Morphometric Evaluation of Thoracolumbar Spinal Canal and Cord by Magnetic Resonance Imaging in Normal Small-Breed Dogs.

Thoracolumbar intervertebral disc disease (IVDD) is the most common cause of spinal injury in dogs. MRI has been considered the gold standard for neurologic diagnosis, but studies focusing on the thoracolumbar spinal canal and spinal cord using MRI in small-breed dogs are limited. Therefore, this study aimed to establish an MRI reference range for the spinal cord and canal measurements (height, width, cord-to-canal ratio of height, width, cross-sectional area (CSA)) of each intervertebral disc level from T11 to L5 (total of seven levels) on transverse T2-weighted images in normal small-breed dogs. We hypothesized that the spinal cord and spinal canal measurements might vary according to the body weight and age. The width and height of the spinal cord and canal increased as the body weight increased at all levels (p < 0.05). The cord-to-canal ratio of the width showed a negative correlation to the body weight at all levels. The cord-to-canal ratio of the height did not show any correlation to the body weight at all levels. All measurements (height, width, cord-to-canal ratio of height, width, CSA) did not show any statistical correlation between the groups subdivided by age. These measurements could serve as a morphometric baseline for thoracolumbar spinal diseases and clinical research in small-breed dogs.

Unraveling trajectories from aplastic anemia to hematologic malignancies: genetic and molecular insights.

Background: Aplastic anemia (AA), characterized by hematopoietic stem cell deficiency, can evolve into different hematologic malignancies. Our understanding of the genetic basis and mechanisms of this progression remains limited. Methods: We retrospectively studied 9 acquired AA patients who later developed hematologic malignancies. Data encompassed clinical, laboratory, karyotype, and next-generation sequencing (NGS) information. We explored chromosomal alterations and mutation profiles to uncover genetic changes underlying the transition. Results: Nine AA patients developed myelodysplastic syndrome (seven patients), acute myeloid leukemia (one patient), or chronic myelomonocytic leukemia (one patient). Among eight patients with karyotype results at secondary malignancy diagnosis, monosomy 7 was detected in three. Trisomy 1, der(1;7), del(6q), trisomy 8, and del(12p) were detected in one patient each. Among three patients with NGS results at secondary malignancy diagnosis, KMT2C mutation was detected in two patients. Acquisition of a PTPN11 mutation was observed in one patient who underwent follow-up NGS testing during progression from chronic myelomonocytic leukemia to acute myeloid leukemia. Conclusion: This study highlights the genetic dynamics in the progression from AA to hematologic malignancy. Monosomy 7's prevalence and the occurrence of PTPN11 mutations suggest predictive and prognostic significance. Clonal evolution underscores the complexity of disease progression.

O- and N-Methyltransferases in benzylisoquinoline alkaloid producing plants.

BACKGROUND: Secondary metabolites such as benzylisoquinoline alkaloids (BIA) have attracted considerable attention because of their pharmacological properties and potential therapeutic applications. Methyltransferases (MTs) can add methyl groups to alkaloid molecules, altering their physicochemical properties and bioactivity, stability, solubility, and recognition by other cellular components. Five types of O-methyltransferases and two types of N-methyltransferases are involved in BIA biosynthesis. OBJECTIVE: Since MTs may be the source for the discovery and development of novel biomedical, agricultural, and industrial compounds, we performed extensive molecular and phylogenetic analyses of O- and N-methyltransferases in BIA-producing plants. METHODS: MTs involved in BIA biosynthesis were isolated from transcriptomes of Berberis koreana and Caulophyllum robustum. We also mined the methyltransferases of Coptis japonica, Papaver somniferum, and Nelumbo nucifera from the National Center for Biotechnology Information protein database. Then, we analyzed the functional motifs and phylogenetic analysis. RESULT: We mined 42 O-methyltransferases and 8 N-methyltransferases from the five BIA-producing plants. Functional motifs for S-adenosyl-L-methionine-dependent methyltransferases were retained in most methyltransferases, except for the three O-methyltransferases from N. nucifera. Phylogenetic analysis revealed that the methyltransferases were grouped into four clades, I, II, III and IV. The clustering patterns in the phylogenetic analysis suggested a monophyletic origin of methyltransferases and gene duplication within species. The coexistence of different O-methyltransferases in the deep branch subclade might support some cases of substrate promiscuity. CONCLUSIONS: Methyltransferases may be a source for the discovery and development of novel biomedical, agricultural, and industrial compounds. Our results contribute to further understanding of their structure and reaction mechanisms, which will require future functional studies.

Whole Blood Viscosity Reference Intervals and Its Correlation with Hematology and Serum Chemistry in Cats Using Scanning Capillary Method.

Whole blood viscosity, a hemorheological factor, is currently used for diagnosis, as it is correlated with various vascular diseases that are difficult to diagnose early with a general blood test. It was determined that it was necessary to set reference intervals for further studies and utilization of whole blood viscosity in cats, a representative companion animal, and this study was conducted. Fifty healthy cats were recruited for the study, and whole blood viscosity, complete blood count, and serum chemistry tests were performed. The reference intervals of whole blood viscosity were 15.169 to 43.684 cP at a shear rate of 1 s-1 reflecting diastole, and 3.524 to 5.544 cP at a shear rate of 300 s-1 reflecting systole. Red blood cells, hematocrit, hemoglobin, white blood cells, and neutrophils in the complete blood count, and total protein, albumin, globulin, and cholesterol in the serum chemistry were significantly correlated with whole blood viscosity. The results of this study set the reference intervals of whole blood viscosity for healthy cats in a wide shear rate range that has not yet been fully established, and its correlation with other blood indicators investigated.

In-situ δ18O and 87Sr/86Sr proxies in an unconformable clastic unit at the Ordovician-Silurian transition.

Clastic successions found in the carbonate platform of continental margin during the Ordovician-Silurian Transition (OST) period are archives for interpreting paleo-depositional systems. Here, we report in-situ δ18Oquartz and 87Sr/86Srcarbonate isotope chemo-stratigraphy for an unconformable clastic unit from the Cathaysia terrane that rifted off the Gondwana Supercontinent in the Early Paleozoic Era. Our results suggest a depositional proxy and model for geological events attributed to rapid changes in the sedimentary environment during the OST period. Importantly, these results present crucial clues that infer the influence of Paleo-Tethys Sea opening, global eustatic regression, and rapid sedimentary provenance change. Our study provides insight into paleo-tracer that could be a key method for interpreting depositional system of carbonate platform based on in-situ mineral isotope chemo-stratigraphy that preserves the original value of provenance and geochemical condition.

Comparison of patellofemoral contact pressure after semi-cylindrical recession trochleoplasty and trochlear block recession in feline cadavers.

Introduction: The purpose of this study was to compare the changes in the patellofemoral joint (PFJ) contact mechanisms of the normal state, trochlear hypoplasia model and after performing trochleoplasty on the hypoplasia model in feline cadavers. Methods: Twenty normal pelvic limbs were acquired from the 10 feline cadavers. First, the PFJ contact mechanisms were measured in normal state, then trochlear hypoplasia models were created using customized trochlear ridge cutting guides. After measuring PFJ contact mechanisms in the trochlear hypoplasia models, they were divided into two groups and performed semi-cylindrical recession trochleoplasty (SCRT) and trochlear block recession (TBR) were performed, respectively. After that, the PFJ contact mechanisms were measured and the values of the 4 groups (normal state, trochlear hypoplasia, SCRT, TBR) were compared. Results: The trochlear hypoplasia group showed increased contact pressure and decreased contact areas compared to the normal state group. In the groups that underwent tracheoplasty (SCRT and TBR), PFJ contact mechanisms were recovered similarly to that of the normal state group. The PFJ of the SCRP group was measured similar to that of the normal group than that of the TBR group. Discussion: Tracheoplasty can be useful in restoring PFJ contact mechanisms and SCRT can be considered as a good alternative to the conventional methods of trochleoplasty.

Training-induced circuit-specific excitatory synaptogenesis in mice is required for effort control.

Synaptogenesis is essential for circuit development; however, it is unknown whether it is critical for the establishment and performance of goal-directed voluntary behaviors. Here, we show that operant conditioning via lever-press for food reward training in mice induces excitatory synapse formation onto a subset of anterior cingulate cortex neurons projecting to the dorsomedial striatum (ACC→DMS). Training-induced synaptogenesis is controlled by the Gabapentin/Thrombospondin receptor α2δ-1, which is an essential neuronal protein for proper intracortical excitatory synaptogenesis. Using germline and conditional knockout mice, we found that deletion of α2δ-1 in the adult ACC→DMS circuit diminishes training-induced excitatory synaptogenesis. Surprisingly, this manipulation does not impact learning but results in a significant increase in effort exertion without affecting sensitivity to reward value or changing contingencies. Bidirectional optogenetic manipulation of ACC→DMS neurons rescues or phenocopies the behaviors of the α2δ-1 cKO mice, highlighting the importance of synaptogenesis within this cortico-striatal circuit in regulating effort exertion.

Application of topical rocuronium bromide dosing by ocular size in four species of wild birds.

BACKGROUND: Rocuronium bromide has been evaluated as a mydriatic agent in birds, but the species applied were limited and the dose and effect were variable. OBJECTIVE: This study aims to evaluate the efficacy of topical rocuronium bromide as mydriatics in 4 species according to horizontal palpebral fissure length: Feral pigeon (Columba livia), Common kestrel (Falco tinnunculus), Northern boobook (Ninox japonica), and Eurasian eagle owl (Bubo bubo). METHODS: A total of 32 birds (8 for each species) were included as pre-releasing examination. Rocuronium bromide was instilled in one randomly selected eye of each bird based on palpebral fissure length criteria (0.5 mg/50 µL for pigeons, 1 mg/100 µL for kestrels and boobook owls, and 2 mg/200 µL for eagle owls). The contralateral eye was used as control and treated with normal saline. After instillation of the drug, pupil diameter, pupillary light reflex, intraocular pressure, heart rate, and respiratory rate were evaluated at 10 min intervals up to 180 min and at 30 min intervals up to 360 min. RESULTS: Statistically significant mydriasis was obtained in all birds (p < 0.001). However, in boobook and eagle owls, marked mydriasis persisted until 360 min. Side effects including corneal erosion and lower eyelid paralysis were common, which was observed in 26/32 birds. Blepharospasm was also noted during this study. No systemic adverse signs were observed. CONCLUSIONS: Rocuronium bromide could be a good mydriatics option for 4 species of birds, however, further studies are needed to find lowest effective dose to reduce drug-related side effects.

The role of the parafascicular thalamic nucleus in action initiation and steering.

The parafascicular (Pf) nucleus of the thalamus has been implicated in arousal and attention, but its contributions to behavior remain poorly characterized. Here, using in vivo and in vitro electrophysiology, optogenetics, and 3D motion capture, we studied the role of the Pf nucleus in behavior using a continuous reward-tracking task in freely moving mice. We found that many Pf neurons precisely represent vector components of velocity, with a strong preference for ipsiversive movements. Their activity usually leads velocity, suggesting that Pf output is critical for self-initiated orienting behavior. To test this hypothesis, we expressed excitatory or inhibitory opsins in VGlut2+ Pf neurons to manipulate neural activity bidirectionally. We found that selective optogenetic stimulation of these neurons consistently produced ipsiversive head turning, whereas inhibition stopped turning and produced downward movements. Taken together, our results suggest that the Pf nucleus can send continuous top-down commands that specify detailed action parameters (e.g., direction and speed of the head), thus providing guidance for orienting and steering during behavior.

Isolation and Characterization of the Genes Involved in the Berberine Synthesis Pathway in Asian Blue Cohosh, Caulophyllum robustum.

Caulophyllum robustum, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of C. robustum, and this is the first report on berberine in this species. Transcriptome analysis was conducted for the characterization of berberine biosynthesis genes in C. robustum, in which, all the genes for berberine biosynthesis were identified. From 40,094 transcripts, using gene ontology (GO) analysis, 26,750 transcripts were assigned their functions in the categories of biological process, molecular function, and cellular component. In the analysis of genes expressed in different tissues, the numbers of genes in the categories of intrinsic component of membrane and transferase activity were up-regulated in leaves versus stem. The berberine synthesis genes in C. robustum were characterized by phylogenetic analysis with corresponding genes from other berberine-producing species. The co-existence of genes from different plant families in the deepest branch subclade implies that the differentiation of berberine synthesis genes occurred early in the evolution of berberine-producing plants. Furthermore, the copy number increment of the berberine synthesis genes was detected at the species level.

Ex Vivo Biomechanical Assessment of Various Repair Techniques in a Rabbit Calcaneal Tendon Avulsion Model: Application of Polycaprolactone Plate.

This study was aimed at evaluating the biomechanical properties and gapping characteristics of tendon repair methods using a combination of a three-loop pulley (3LP) pattern, a titanium plate, and a polycaprolactone (PCL) plate in a rabbit gastrocnemius tendon (GT) model (n = 50). GTs were randomly assigned to five groups (n = 10/group). Transected GTs were repaired with a 3LP pattern alone or in conjunction with an epitendinous suture (ES), a 5-hole 1 mm PCL plate, a 5-hole 2 mm PCL plate, or a 5-hole 1.5 mm titanium plate. The yield, peak, and failure force, as well as the occurrence and force of 1-mm and 3-mm gapping were examined. The mean yield, peak, and failure force of the 3LP + titanium plate group were higher than that of other groups. The biomechanical properties of a 3LP + a 2 mm PCL plate were similar to 3LP + ES constructs in this model. In all specimens in all groups, 1 mm gap formation was observed. The frequency of 3 mm gap formation was 70% and 90% in the 3LP + 2 mm PCL plate group and the 3LP + 1.5 mm titanium plate group, respectively. Additional studies evaluating PCL plates to determine the effect on the healing and blood supply of tendon are needed.

Accuracy of a 3-dimensionally printed custom endoscopy port for minimally invasive ventral slot decompression in dogs: A cadaveric study.

OBJECTIVE: To evaluate the accuracy of a 3-dimensionally (3D)-printed custom endoscopy port (3DEP) for minimally invasive cervical ventral slot decompression. STUDY DESIGN: Cadaveric study. ANIMALS: Fifteen cadavers of dogs weighing between 3.1 and 34.4 kg. METHODS: Minimally invasive cervical ventral slots were created using a 3DEP and an endoscopic system at the C3-C4 intervertebral disc space in each dog by 1 experienced and 1 inexperienced surgeon. Postoperative computed tomography was performed to compare the planned and postoperative screw trajectories (angle, entry point, exit point, and length of the screw entering the spinal canal) and quantify slot formation dimensions. RESULTS: Thirty screws were inserted in 30 vertebral bodies. Mean screw angle deviation was less than 2.5°, entry and exit point deviation was less than 1.6 mm, and length of the screw entering the spinal canal was less than 0.6 mm. No differences were identified between the experienced and inexperienced surgeons. Ventral slot length ratio was 30.15 ± 1.86 for the experienced surgeon and 29.38 ± 1.61 for the inexperienced surgeon (p = .372). The mean ventral slot width ratio was 45.60 ± 1.80 for the experienced surgeon and 47.20 ± 1.54 for the inexperienced surgeon (p = .261). CONCLUSION: Screw positioning and creation of ventral slots were accurately performed using the 3DEP by both inexperienced and experienced surgeons. CLINICAL SIGNIFICANCE: The use of a 3DEP for minimally invasive cervical ventral slot decompression may be an alternative to the conventional ventral slot in dogs. Additional studies are needed to evaluate efficacy and safety.

Differential Encoding of Trace and Delay Fear Memory in the Entorhinal Cortex.

Trace fear conditioning is characterized by a stimulus-free trace interval (TI) between the conditioned stimulus (CS) and the unconditioned stimulus (US), which requires an array of brain structures to support the formation and storage of associative memory. The entorhinal cortex (EC) has been proposed to provide essential neural code for resolving temporal discontinuity in conjunction with the hippocampus. However, how the CS and TI are encoded at the neuronal level in the EC is not clear. In Exp. 1, we tested the effect of bilateral pre-training electrolytic lesions of EC on trace vs. delay fear conditioning using rats as subjects. We found that the lesions impaired the acquisition of trace but not delay fear conditioning confirming that EC is a critical brain area for trace fear memory formation. In Exp. 2, single-unit activities from EC were recorded during the pre-training baseline and post-training retention sessions following trace or delay conditioning. The recording results showed that a significant proportion of the EC neurons modulated their firing during TI after the trace conditioning, but not after the delay fear conditioning. Further analysis revealed that the majority of modulated units decreased the firing rate during the TI or the CS. Taken together, these results suggest that EC critically contributes to trace fear conditioning by modulating neuronal activity during the TI to facilitate the association between the CS and US across a temporal gap.

Comparison of dorsal and medial arthroscopic approach to canine coxofemoral joint: a cadaveric study.

BACKGROUND: Arthroscopic exploration of ventromedial part of canine coxofemoral joint is limited in conventional dorsal approach. OBJECTIVES: We evaluated the efficacy of a medial arthroscopic approach to the coxofemoral joint of dogs by analyzing the joint visible area and performing a safety analysis. METHODS: Arthroscopic approaches to the coxofemoral joint were made in five cadavers using a traditional (dorsal) and novel (medial) approach. Three observers scored the visible area of images and videos of the acetabulum and femur. A safety analysis was performed via dissection of the medial hind limb. The distance between neurovascular structures and arthroscopic portals was measured. RESULTS: The acetabulum was more visible in the dorsal than in the medial approach, with mean visualization scores of 16 ± 0.00 and 11.83 ± 1.26, respectively. The medioventral side of the femur was significantly more visible in the medial than in the dorsal approach, with mean visualization scores of 3.9 ± 0.99 and 6.93 ± 0.58, respectively. Safety analysis confirmed the medial portal site was safe, provided that the surgeon has comprehensive knowledge of the joint. The minimum distance from the arthroscopic medial portals to the nearest neurovascular structures was 2.5 mm. CONCLUSIONS: A medial arthroscopic approach to the canine coxofemoral joint has potential clinical application. Dorsal and medial approaches differ significantly and have distinct purposes. The medial approach is useful to access the ventromedial joint, making it an eligible diagnostic method for an arthroscopic evaluation of this area.

A one-photon endoscope for simultaneous patterned optogenetic stimulation and calcium imaging in freely behaving mice.

Optogenetics and calcium imaging can be combined to simultaneously stimulate and record neural activity in vivo. However, this usually requires two-photon microscopes, which are not portable nor affordable. Here we report the design and implementation of a miniaturized one-photon endoscope for performing simultaneous optogenetic stimulation and calcium imaging. By integrating digital micromirrors, the endoscope makes it possible to activate any neuron of choice within the field of view, and to apply arbitrary spatiotemporal patterns of photostimulation while imaging calcium activity. We used the endoscope to image striatal neurons from either the direct pathway or the indirect pathway in freely moving mice while activating any chosen neuron in the field of view. The endoscope also allows for the selection of neurons based on their relationship with specific animal behaviour, and to recreate the behaviour by mimicking the natural neural activity with photostimulation. The miniaturized endoscope may facilitate the study of how neural activity gives rise to behaviour in freely moving animals.

Case report: Reconstruction of a complex maxillofacial gunshot defect using a titanium patient-specific implant in a dog.

This report describes the surgical reconstruction of large maxillofacial defect caused by a short-range gunshot injury in a dog using titanium patient-specific implant (PSI). A 3-year-old male Wolf Shepherd was admitted for a large right facial defect with right nasal cavity exposure caused by a gunshot injury. Radiographic examination revealed severe loss of the right maxillary, nasal, and incisive bones, multiple fractures of both left and right palatine bones, and a comminuted fracture of the right mandible. Initial surgical procedure included computed tomography (CT) imaging for three-dimensional (3D) implant design. Open wound management was maintained for 18 days until the fresh granulation tissue fully covered the wound bed. The implant was designed in a "hand grasping shape" to cover the defect, align multiple fractured palatine bones, and make a snap fit function. Multiple holes, including cortical screw holes, were added to the final design. The implant was printed on a titanium alloy. Surgical application of titanium PSI was performed 19 days after the primary surgery. A free sublingual mucosal graft was used to reconstruct the mucosal layer of the right nasal cavity. The mucosa was then covered with collagen membrane to strengthen the structure of the nasal cavity. Blunt dissection of the hard palate mucoperiosteum above the palatine process and palatine bones, soft tissue above the maxilla was performed, and the 3D printed titanium implant was fastened in a preplanned position. The facial soft tissue defect was reconstructed, and the titanium PSI was covered using an angularis oris cutaneous flap. Partial flap necrosis occurred in the rostral aspect, and the wound was managed to heal by a second intension. Flap dehiscence at the junction of the flap and hard palate mucoperiosteum occurred with exposure of the implant 2 days postoperatively. Multiple attempts to close the defect failed, and the owner wanted to stop treatment. Healthy granulated tissue was observed proximal to the implant. The defect no longer increased in size and did not show any noticeable complications related to the defect at 60 days after titanium PSI application, and the dog was discharged. Six months post-operatively, the dog remained active with great appetite, gained weight, and showed acceptable facial symmetry without enlargement of the implant exposure or any implant-related problems.

Comparative Transcriptomics for Genes Related to Berberine and Berbamine Biosynthesis in Berberidaceae.

Berberine and berbamine are bioactive compounds of benzylisoquinoline alkaloids (BIAs) present in Berberis species. The contents of berbamine are 20 times higher than berberine in leaf tissues in three closely related species: Berberis koreana, B. thunbergii and B. amurensis. This is the first report on the quantification of berberine compared to the berbamine in the Berberis species. Comparative transcriptome analyses were carried out with mRNAs from the leaf tissues of the three-species. The comparison of the transcriptomes of B. thunbergii and B. amurensis to those of B. koreana, B. thunbergii showed a consistently higher number of differentially expressed genes than B. amurensis in KEGG and DEG analyses. All genes encoding enzymes involved in berberine synthesis were identified and their expressions were variable among the three species. There was a single copy of CYP80A/berbamunine synthase in B. koreana. Methyltransferases and cytochrome P450 mono-oxidases (CYPs) are key enzymes for BIA biosynthesis. The current report contains the copy numbers and other genomic characteristics of the methyltransferases and CYPs in Berberis species. Thus, the contents of the current research are valuable for molecular characterization for the medicinal utilization of the Berberis species.

Whole-genome sequencing revealed different demographic histories among the Korean endemic hill pigeon (Columba rupestris), rock pigeon (Columba livia var. domestica) and oriental turtle dove (Streptopelia orientalis).

BACKGROUND: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES: Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. RESULTS: The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. CONCLUSION: The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5-1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.