An algorithm to generate 2D bathymetry of an Alpine river for habitat suitability assessment

Here we present an original approach to generate 2D high detail riverbed based on a drone photogrammetric survey, and RTK bathymetry measurements for Mera river in the Italian Alps. The aim is to better represent macro-roughness and riverbed structure of the river, also extending it to an ungauged area. Specifically, we apply a step-by-step approach. I) Depth and average slope of the riverbed were calculated from bathymetry data. II) Thus, a trapezoidal channel with constant slope and variable width was defined using the drone images. III) Riffle-pool sequence was assessed as a function of river width and applied to the generated channel. IV) Finally, the semi-random Perlin Noise was added to recreate riverbed irregularities in the natural stream. HEC-RAS 2D hydraulic software was then implemented to assess spatialized water depth and velocity. The proposed methodology could be quite relevant in river hydraulics to decouple roughness coefficient from water submergence, and in Physical Habitat Simulation Model (PHABSIM), where the dependency of the output is not linear with hydraulic parameters (i.e. water depth and velocity). Indeed, we apply PHABSIM for a case study of a stretch of the river and results are compared with a previous environmental study for Mera river.

Concurrent Occurrence of Infectious Bursal Disease and Multicausal Respiratory Infections Caused by Newcastle Disease and Avian Metapneumovirus in Broilers

Control strategy of respiratory complex infections should address precipitating and predisposing causative agents in general and immunosuppressive agents in particular. In both clinical and subclinical forms, infectious bursal disease virus (IBDV) is one of the most immunosuppressive diseases of young chickens. This study aimed to investigate the concurrent occurrence of subclinical infectious bursal disease (IBD) and multicausal respiratory complex infections caused by Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) in broilers. In this study, 800 tissue samples (e.g., trachea, cecal tonsil, bursa of Fabricius, and spleen) and 400 sera samples were collected from broilers with confirmed respiratory signs selected from 20 broiler farms in west Azerbaijan province, Iran, from October 2018 to February 2019. Pathogens in the tissue samples were detected using RT-PCR for the VP2 gene of IBDV, F gen of NDV, and N gene of aMPV. The amplified products were sequenced afterward. At the end of the husbandry period, sera samples were used to detect antibodies against IBDV, aMPV, and NDV using ELISA and HI tests. Molecular results showed that the 45% (9/20), 30% (6/20), and 15% (3/20) of tissue samples were positive for IBDV, NDV, and aMPV, respectively. Regarding co-infection, 5% (1/20) of farm isolates were positive for IBD and ND, while 10% (2/20) of farms isolates were positive for IBD and aMPV. Co-infection of IBD, ND, and aMPV was not detected in farm isolates. Serological results indicated that the IBD co-infected flocks had almost higher (P<0.05) antibody titers against IBD; however, IBDV-NDV co-infected flocks and IBDV-aMPV co-infected flocks had lower antibody titer against NDVand aMPV, respectively. It can be concluded that lower antibody titer against ND and aMPV in IBD-ND and IBD-aMPV co-infections indicated suppressive effects of IBD on these diseases. Therefore, vaccination against IBD even in regions without clinical form of IBD is inevitable for the reduction of immunosuppressive effects of subclinical IBD on immune responses against these diseases.

HBB mutations and HbA2 level: Escaping the carrier screening programs

HbA2 level alone for beta thalassemia trait may not be accurate and reliable even without iron deficiency so molecular genetic testing is important and should be considered for some individuals.

Novel disease-causing variants in a cohort of Iranian patients with metachromatic leukodystrophy and in silico analysis of their pathogenicity

OBJECTIVE

Metachromatic leukodystrophy (MLD) is an autosomal recessive leukodystrophy caused by deficiency of aryl sulfatase A (ASA) activity affecting the nervous system. MLD and mutations in ARSA have not been widely studied in non-European cohorts. The genotype-phenotype spectrum of MLD patients was investigated in this study of a cohort of Iranian leukodystrophy patients. In silico analysis was performed to investigate the pathogenicity of the variants.

METHODS

Genetic analysis for 25 patients was performed with direct sequencing of the ARSA gene. The missense variants underwent in silico analysis to characterize the pathogenicity based on predicted structural and stability changes.

RESULTS

19 patients had variants in ARSA genes, including 18 homozygotes and one compound heterozygote individual. In 6 individuals no mutations were found in ARSA gene, suggesting an alternative cause of their leukodystrophy. We found 5 novel disease causing variants: p.Phe64Ile, p.Ser292Alafs*34, p.Arg99Profs*35, p.Phe400Leu and p.Leu429Pro. 32 % of the patients had p.Gly311Ser substitution and resulted in juvenile MLD type. Different in silico analysis showed variable pathogenic effect for the variants.

CONCLUSION

c.931 G > A (p.Gly311Ser) and c.465 + 1 G > A variants are the most frequent alleles among Iranian MLD patients and five mutations appear to be confined to the Iranian patients. Population screening for these variants may be helpful to reduce the burden of the disease in this part of the world.

Safety and Efficacy of Early Oral Feeding after Liver Transplantation with Roux-en-Y Choledochojejunostomy: A Single-Center Experience

BACKGROUND

Early oral feeding, as one of the most important components of multimodal strategies referred to as Enhanced Recovery After Surgery (ERAS), is now widely adopted for optimization of post-operative recovery of surgical patients.

OBJECTIVE

To assess ERAS outcome in patients who underwent liver transplantation in our center.

METHODS

In a prospective study, patients who underwent liver transplantation from April 2015 to June 2018 at Imam Khomeini Hospital Complex, affiliated to Tehran University of Medical Sciences, Tehran, Iran, were enrolled in this study. Serum albumin, total iron-binding capacity (TIBC), and course of hospital stay were assessed.

RESULTS

39 (23 male) patients who underwent choledochojejunostomy with Roux-en-Y anastomosis for liver transplantation were enrolled. The mean±SD pre-operative serum albumin and TIBC levels of patients were 3.0±0.6 (range: 1.9-4.1) g/dL and 304±75 (range: 154.0-437.0) µg/dL, respectively. The mean±SD time between the end of operation and starting oral feeding was 11.6±1.8 (range: 9.0-15.0) hours. All patients tolerated early oral feeding with liquids followed by solid foods; no vomiting reported in patients. Overall, patient survival rates at one month and three months were 89.7% and 89.7%, respectively. In our study, no leak of anastomosis was reported.

CONCLUSION

There was no major harm for ERAS after liver transplantation and it might be even helpful as in colorectal surgeries. As seen in our study, oral feeding was started as soon as possible after the end of operation in almost all patients and all of them tolerated early oral feeding. No one had vomiting or nausea.

Antibacterial, antibiofilm and antiquorum sensing effects of Thymus daenensis and Satureja hortensis essential oils against Staphylococcus aureus isolates

AIMS

The present study was conducted to investigate the effects of Thymus daenensis and Satureja hortensis essential oils (EOs) on the planktonic growth, biofilm formation and quorum sensing (QS) of some Staphylococcus aureus isolates (strong biofilm producers).

METHODS AND RESULTS

Minimum inhibitory concentration (MIC) of the EOs, inhibition of biofilm formation as well as disruption of preformed Staph. aureus biofilms were assessed. The antibiofilm activity of the EOs was determined using microtitre plate test (MtP) and scanning electron microscope (SEM). The QS inhibitory activity was also examined on the pregrown biofilms by gene expression analysis using quantitative real-time RT-polymerase chain reaction (PCR) of hld gene (RNAIII transcript). Moreover, tetrazolium-based colorimetric assay (MTT) was performed to detect cytotoxic effects of these EOs on the Vero cell line. Finally, the major components of the tested EOs were determined using Gas Chromatography-Mass Spectrometry (GC-MS). The MICs of T. daenensis and S. hortensis EOs against planktonic cells of the isolates were 0·0625 and 0·125 μl ml^-1 respectively. The minimum bactericidal concentrations for both of the EOs was 0·125 μl ml^-1 . The MtP test showed a significant inhibitory effect of the EOs on the biofilm formation and disruption at sub-MIC concentrations. These results were confirmed by SEM. Real-time PCR revealed a significant down-regulation of hld gene following treatment with MIC/2 concentration of S. hortensis EO. GC-MS analysis showed that carvacrol, terpinene and thymol were the major components of the applied EOs.

CONCLUSIONS

As selected EOs did not show significant cytotoxic effects even up to tenfold of MIC concentration, the applied EOs seem to be good candidates for preventing of biofilm formation of Staph. aureus cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study introduced T. daenensis and S. hortensis EOs as new antibiofilm, and S. hortensis EO as anti-QS herbal agents with natural origin against Staph. aureus.

Capturing Spatial Variability of Biogeochemical Mass Exchanges and Reaction Rates in Wetland Water and Soil through Model Compartmentalization

A common phenomenon observed in natural and constructed wetlands is short-circuiting of flow and formation of stagnant zones that are only indirectly connected with the incoming water. Biogeochemistry of passive areas is potentially much different than that of active zones. In the research reported in this paper, the spatial resolution of a previously developed wetland nutrient cycling model was improved in order to capture the spatial variability of concentrations and reaction rates regarding nitrogen and carbon cycles throughout active and passive zones of wetlands. The upgraded model allows for several compartments in the horizontal domain, with all neighboring compartments connected through advective and dispersive/diffusive mass transport. The model was applied to data collected from a restored wetland in California that was characterized by the formation of a large stagnant zone at the southern end of the wetland due to close vicinity of the inlet and outlet structures in the northern end. Mass balance analysis revealed that over the course of the research period, about 23.4±3.9% of the incoming total nitrogen load was removed or retained by the wetland. It was observed that mass of all exchanges (physical and biogeochemical) regarding nitrogen cycling decreased along the activity gradient from active to passive zones. Model results also revealed that anaerobic processes become more significant along the activity gradient towards passive areas.

Modeling Nitrogen and Carbon dynamics in wetland soils and water using a mechanistic wetland model

In this article, extension and application to variably-saturated wetland conditions of a process-based wetland model, namely WetQual is demonstrated. The new model described in this article is an improved version of an earlier model, which was only capable of capturing nutrient dynamics in continuously ponded wetlands. The upgraded model is capable of simulating nutrient cycling and biogeochemical reactions in both ponded and unsaturated zones of the wetland. To accomplish this goal, a comprehensive module for tracking water content in wetland soil was implemented in the model, and biogeochemical relationships were added to explain cycling of nitrogen (N) and carbon (C) in variably saturated zones of wetlands. The developed model was applied to a small, restored wetland receiving agricultural runoff, located on Kent Island, Maryland. On average, during the two year study period, the ponded compartment of the study wetland covered 65% of the total 1.2 ha area. Through mass balance analysis, it was revealed that the mass of nitrogen lost to denitrification at the variably saturated compartment of the study wetland was about 3 times higher than that of the ponded compartment (32.7 ± 29.3 kg vs. 9.5 ± 5.5 kg) whereas ammonia volatilization at the variably saturated compartment was a fraction of that of ponded compartment (1.2 ± 1.9 kg vs. 11.3 ± 11.8 kg). Sensitivity analysis showed that cycling of carbon related constituents in variably saturated compartment had high sensitivity to temperature and available soil moisture.

RNAi-induced silencing in floral tissues of Petunia hybrida by agroinfiltration: a rapid assay for chalcone isomerase gene function analysis

Variegation in flower color is commonly observed in many plant species and also occurs on Petunia (Petunia hybrida) as an ornamental plant. Variegated plants are of highly valuable in the floricultural market. Agroinfiltration is an Agrobacterium-mediated transient assay for the analysis of gene function and genetic modification in leaves, flowers and fruit tissues of various plants. Transient RNAi-induced silencing by agroinfiltration has been developed in leaves and fruits of several plant species. Here we report the establishment of a transient hairpin RNAi-induced silencing system for color modification assay in floral tissues of Petunia with different colors. chiRNAi construct was cloned into the pBI121 vector under the control of 35S promoter. Transient RNA silencing of chi in the floral tissues of Petunia was induced by delivering 530 bp chi hairpin RNAs (hpRNAs) into the petals of flowers using agroinfiltration. Impaired anthocyanin accumulation and reduction of endogenous mRNAs of the corresponding targets were observed in the infiltrated areas of the petals of four colors of Petunia. Silencing of the endogenous chi mRNAs was highly effective in reduction of chi gene and anthocyanin accumulation. This transient silencing system is a prototype for modification of the anthocyanin biosynthetic pathway in Petunia through chi gene suppression.

A rare case of a myofibroma presenting on the tongue

Myofibromas are benign neoplasms of myofibroblastic origin, rarely encountered in the oral cavity. Limited awareness of the clinical features of these lesions risks misdiagnosis of more sinister pathology. The objective of this report is to highlight the potential diversity of oral lesions by describing an uncommon presentation of a myofibroma. The case reveals the diagnostic difficulties encountered, along with postoperative complications, which exemplify the remarkable healing capacity of the oral cavity.

Expression and lysosomal targeting of CLN7, a major facilitator superfamily transporter associated with variant late-infantile neuronal ceroid lipofuscinosis

Neuronal ceroid lipofuscinoses (NCLs) constitute a group of progressive neurodegenerative disorders resulting from mutations in at least eight different genes. Mutations in the most recently identified NCL gene, MFSD8/CLN7, underlie a variant of late-infantile NCL (vLINCL). The MFSD8/CLN7 gene encodes a polytopic protein with unknown function, which shares homology with ion-coupled membrane transporters. In this study, we confirmed the lysosomal localization of the native CLN7 protein. This localization of CLN7 is not impaired by the presence of pathogenic missense mutations or after genetic ablation of the N-glycans. Expression of chimeric and full-length constructs showed that lysosomal targeting of CLN7 is mainly determined by an N-terminal dileucine motif, which specifically binds to the heterotetrameric adaptor AP-1 in vitro. We also show that CLN7 mRNA is more abundant in neurons than astrocytes and microglia, and that it is expressed throughout rat brain, with increased levels in the granular layer of cerebellum and hippocampal pyramidal cells. Interestingly, this cellular and regional distribution is in good agreement with the autofluorescent lysosomal storage and cell loss patterns found in brains from CLN7-defective patients. Overall, these data highlight lysosomes as the primary site of action for CLN7, and suggest that the pathophysiology underpinning CLN7-associated vLINCL is a cell-autonomous process.

Role of dipstick in detection of haeme pigment due to rhabdomyolysis in victims of Bam earthquake

Avoiding life-threatening complications of rhabdomyolysis depends on early diagnosis and prompt management. The aim of this study was to evaluate the role of urinary dipstick test in the detection of haeme pigment in patients who were at risk of acute renal failure (ARF) due to rhabdomyolysis after suffering injury in the Bam earthquake. Serum creatine phosphokinase (CPK) level was used as the gold standard for prediction of ARF. ARF developed in 8 (10%) of 79 patients studied. We found no significant differences in the sensitivity, specificity and accuracy of dipstick urine and serum CPK tests for identifying patients who were at risk of ARF. However, dipstick urine test is an easy test that can be performed quickly at an earthquake site.

Rapid detection of Salmonella enteritidis by PCR amplification of the SefA gene and it's cloning

The emergence of Salmonella enteritidis as an important food-borne pathogenesis in humans, demands the development of novel detection and intervention strategies. It is generally accepted that fimbriae are an important factor in bacterial survival and persistence in the host. This study is directed towards the method of amplifying and cloning the SefA gene, which encode Salmonella enteritidis fimbrial protein. Strains used for these studies were S. enteritidis (E3), which were collected from Kermanshah region. Chromosomal DNA was extracted by boiling method and PCR reaction was performed and single band of 511 bp amplified by SefA-F and SefA-R primers. The resulting PCR product was inserted into the cloning vector (pTZ57R/T). In order to amplify the recombinant plasmid, E. coli DH5 alpha bacteria were transformed with SefA-pTZ57R/T. Recombinant clones were identified by blue/white selection and purified recombinant plasmids were indicated by an alkaline lysis procedure. Identity of the SefA-pTZ57R/T product was confirmed by RFLP and sequencing. Nucleotide and protein alignment with BLAST software showed that the sequence of the SefA gene derived from S. enteritidis (E3), which was cloned in the pTZ57R/T vector, was 99% identical to that of the Genbank (L11008). The sequence of the SefA gene from S. enteritidis (E3) differed only in two nucleotides and one amino acid. The cloned SefA gene from S. enteritidis (E3) was submitted to the NCBI Genbank (EF553334).

How accurate is model planning for orthognathic surgery?

The purpose of this study was to evaluate the accuracy of model surgery prediction after orthognathic surgery and to identify possible errors associated with the prediction process. The study included 46 patients who had undergone orthognathic surgical procedures; 22 in Group A who had had a Le Fort I osteotomy; and 24 in Group B who had had a Le Fort I osteotomy and mandibular setback surgery. The immediate postoperative and preoperative lateral cephalograms were analysed to calculate surgical changes; these were compared with those obtained from model surgery prediction and a statistical analysis was undertaken. The maxilla was more under-advanced and over-impacted anteriorly than predicted by model surgery. The amount of mandibular setback was more than that predicted by model surgery. None of the differences between prediction planning and actual surgical changes was statistically significant at p<0.05. Inaccuracy with the face bow recording, the intermediate wafer, and auto-rotation of the mandible in the supine or anaesthetized patient would appear to be the principal reasons for errors. Inaccuracies are associated with the transfer of prediction planning to model surgery planning and prediction, which should be eliminated to improve the accuracy and predictability of orthognathic surgery.

Rapid detection of Potato Y potyvirus in potato farms of Kermanshah using RT-PCR amplification of the P1-protease gene and its cloning

In this study, the RT-PCR method was used to detect the Y virus in potato tubers and leaves. Samples suspicious of virus infection with symptoms of virus infection were gathered from farms in Kermanshah and placed in plastic bags and kept at -80 degrees C temperature in order to maintain the RNA of the virus until extraction. The extraction and purification of RNA were carried out using Tri-Reagent kit. One of the virus genes is the P1 protease gene which codes a proteinase enzyme. This enzyme plays a role in breaking the initial polyprotein. For amplification of this gene three primer, including primer-1, primer-2 and primer-3, were designed and used. Using primer 1 and reverse transcriptase enzyme, cDNA was synthesized and then PCR was performed using the primers 1, 2 and 3. The PCR products were examined by agarose gel electrophoresis (1%). Consequently, two pieces of DNA (400 and 800 bp) were yielded which were identical to the genome DNA sequencing. Thus, the proposed technique is a convenient method for quick and accurate detection of viruses and, therefore, the application of this method for detecting Potato Y virus in potato farms is recommended.