fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences

There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized. Some of these transcripts may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation of such transcripts to find functional non-coding RNA candidates is very costly. Therefore, our primary interest is to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts. We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc. fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available a

Comparative functional analysis of CYP71AV1 natural variants reveals an important residue for the successive oxidation of amorpha-4,11-diene

AbstractArtemisinin is an antimalarial sesquiterpenoid isolated from the aerial parts of the plant Artemisia annua. CYP71AV1, a cytochrome P450 monooxygenase was identified in the artemisinin biosynthetic pathway. CYP71AV1 catalyzes three successive oxidation steps at the C12 position of amorpha-4,11-diene to produce artemisinic acid. In this study, we isolated putative CYP71AV1 orthologs in different species of Artemisia. Comparative functional analysis of CYP71AV1 and its putative orthologs, together with homology modeling, enabled us to identify an amino acid residue (Ser479) critical for the second oxidation reaction catalyzed by CYP71AV1. Our results clearly show that a comparative study of natural variants is useful to investigate the structure–function relationships of CYP71AV1

Distinct Osteogenic Potentials of BMP-2 and FGF-2 in Extramedullary and Medullary Microenvironments

Bone morphogenetic protein-2 (BMP-2) and fibroblast growth factor-2 (FGF-2) have been regarded as the major cytokines promoting bone formation, however, several studies have reported unexpected results with failure of bone formation or bone resorption of these growth factors. In this study, BMP-2 and FGF-2 adsorbed into atellocollagen sponges were transplanted into bone defects in the bone marrow-scarce calvaria (extramedullary environment) and bone marrow-abundant femur (medullary environment) for analysis of their in vivo effects not only on osteoblasts, osteoclasts but also on bone marrow cells. The results showed that BMP-2 induced high bone formation in the bone marrow-scarce calvaria, but induced bone resorption in the bone marrow-abundant femurs. On the other hand, FGF-2 showed opposite effects compared to those of BMP-2. Analysis of cellular dynamics revealed numerous osteoblasts and osteoclasts present in the newly-formed bone induced by BMP-2 in calvaria, but none were seen in either control or FGF-2-transplanted groups. On the other hand, in the femur, numerous osteoclasts were observed in the vicinity of the BMP-2 pellet, while a great number of osteoblasts were seen near the FGF-2 pellets or in the control group. Of note, FCM analysis showed that both BMP-2 and FGF-2 administrated in the femur did not significantly affect the hematopoietic cell population, indicating a relatively safe application of the two growth factors. Together, these results indicate that BMP-2 could be suitable for application in extramedullary bone regeneration, whereas FGF-2 could be suitable for application in medullary bone regeneration

HLA-DRB1 and DQB1 alleles in Japanese type 1 autoimmune hepatitis: The predisposing role of the DR4/DR8 heterozygous genotype

ObjectiveAutoimmune hepatitis (AIH) is a chronic progressive liver disease. AIH is composed predominantly of type 1 in Japanese populations. The genetic and environmental factors are associated with the pathogenesis of AIH. HLA-DRB1*03:01 and *04:01 are associated with type 1 AIH in European and *04:05 in Japanese populations. Here, we conducted an HLA association study in order to find HLA alleles or haplotypes predisposing or protective for Japanese AIH.MethodsHLA-DRB1 and DQB1 genotyping of 360 type 1 AIH patients and 1026 healthy controls was performed.ResultsThe predisposing association of DRB1*04:01 (P = 0.0006, corrected P [Pc] = 0.0193, odds ratio [OR] 2.97, 95% confidence interval [CI] 1.62–5.43), DRB1*04:05 (P = 1.89×10−21, Pc = 5.86×10−20, OR 3.41, 95% CI 2.65–4.38), and DQB1*04:01 (P = 4.66×10−18, Pc = 6.99×10−17, OR 3.89, 95% CI 2.84–5.33) and the protective association of DRB1*13:02 (P = 0.0003, Pc = 0.0080, OR 0.48, 95% CI 0.32–0.72) with Japanese type 1 AIH were observed. An association of the DR4/DR8 heterozygous genotype with Japanese AIH was identified for the first time (P = 3.12×10−9, OR 3.52, 95% CI 2.34–5.29). Susceptible diplotypes were DRB1*04:05-DQB1*04:01/DRB1*08:02-DQB1*03:02 (P = 0.0004, OR 24.77, 95% CI 1.45–424.31) and DRB1*04:05-DQB1*04:01/DRB1*08:03-DQB1*06:01 (P = 1.18×10−6, OR 10.64, 95% CI 3.19–35.46). Serum levels of Immunoglobulin G and Immunoglobulin M, International Autoimmune Hepatitis Group score, positive rate of anti-smooth muscle antibodies, and the rate of definite AIH were higher in AIH patients with DRB1*04:05 than without.ConclusionsThe important roles of specific combinations of DRB1 and DQB1 alleles or haplotypes in the pathogenesis of type 1 AIH were suggested. The association of DR4/DR8 heterozygous genotype suggested the pathologic importance of trans-complementing DQα-β heterodimer molecules encoded by DQA1 allele of one haplotype and the DQB1 allele of the other haplotype, as it was proposed in the HLA association studies of Type 1 diabetes

Dematiaceous fungal keratitis caused by Cladophialophora boppii — A case report

Purpose: To report a rare case of dematiaceous fungal keratitis caused by Cladophialophora boppii (C. boppii) in an immunocompromised patient. Observations: An 83-year-old male with chronic renal failure was referred to the Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan due to persistent corneal epithelial defects (PEDs) in his left eye. Initial examination revealed decreased central corneal sensitivity and decreased tear secretion in that eye, both thought to be associated with herpetic keratitis. Permanent punctal-plug surgery combined with therapeutic soft contact lens wear was performed to treat the PED, which initially healed, yet recurred. Follow-up examination revealed a 1.0-mm-diameter black lesion consistent with the PED site, which subsequently increased in size, so treatment with miconazole solution eye drops, natamycin ophthalmic ointment, and systemic itraconazole was initially performed. Since the region of the lesion had progressed to corneal perforation, corneal transplantation surgery under general anesthesia was scheduled, yet the patient refused to undergo surgery. Mycological testing via DNA sequencing of the internal transcribed spacer of ribosomal DNA regions revealed that the isolate or pathogen was C. boppii. Mycotic keratitis caused by C. boppii was found to be resistant to antifungal drugs. Conclusion and importance: This is a rare case of fungal keratitis caused by C. boppii in an elderly immunocompromised patient

Effect of distance between occupants and insulation performance of window on contaminant distribution in a room with displacement ventilation

In recent years, displacement ventilation system has received much attention in terms of infectious disease control, due to the epidemic of COVID-19 infections. Plume from occupants and the other heat sources is a very important factor for displacement ventilation because it determines the height of the contaminant stratification. Therefore, this paper aims at the effect of distance between occupants on distribution of temperature, contaminant concentration and plume from occupants in CFD analysis at first. The results suggest the specific distance where plume from occupant interfere with each other in the occupied zone. Our results also indicate that other conditions such as human body posture also affect the interference. In addition, since the aforementioned study don't take into account the influence of the temperature of window surface cooled by outside air, we vary the insulation performance of the window and check the concentration in the occupied area. The results are obtained that the amount of contaminants carried by the downward flow from the window to the lower part of the room depends on the insulation performance of the window, which affects the occupied zone

Successful Management of Fungal Keratitis by Alternaria alternata Complicating Mooren’s Ulcer

Mooren’s ulcer is an idiopathic peripheral ulcerative keratitis whose pathogenesis is thought to be due to an autoimmune reaction. The first-line treatment for Mooren’s ulcer is the use of topical steroids, which can be difficult to discontinue. The 76-year-old patient in this case was receiving topical steroids for bilateral Mooren’s ulcer and developed a feathery corneal infiltration and perforation in the left eye. On suspicion of a fungal keratitis complication, we started topical voriconazole treatment and performed lamellar keratoplasty. Topical betamethasone was continued twice a day. The identified causative fungus was Alternaria alternata, which is known to be susceptible to voriconazole. The minimum inhibitory concentration of voriconazole was later proven to be 0.5 μg/mL. After 3 months of treatment, the residual feathery infiltration disappeared and the left vision recovered to 0.7. In this case, topical voriconazole was effective, and the eye was successfully treated with continuing topical steroids. Fungal species identification and antifungal susceptibility test proved helpful for symptom management

Malignant Melanoma with Probable Smooth Muscle Differentiation

Malignant melanomas occasionally exhibit various divergent differentiation types. Of these, smooth muscle differentiation is extremely rare; only 1 case has been reported in the literature until recently. We report an extremely rare case of malignant melanoma with smooth muscle differentiation, which appeared as an amelanotic reddish nodule on the left toe