Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo single-cell analysis using calcofluor - white staining detects high expression phenotype in L. lactis cultures engineered for hyaluronic acid production

Hyaluronic acid (HA) is a biopolymer with wide applications in the field of medicine and cosmetics. Bacterial production of HA has a huge market globally. Certain species of Streptococcus are native producers of HA but they are pathogenic. Therefore, safer organisms such as L. lactis are engineered for HA production. However, there are challenges such as low yield, low molecular weight and polydispersity of HA obtained from these cultures. Optimisation of bioprocess parameters and downstream purification parameters are being addressed to overcome these challenges. We explore these problems from the perspective of microbial heterogeneity, since variations in phenotype affect the yield and properties of the product in a bioreactor. For this perspective, a method to quantitatively assess the occurrence of heterogenous phenotypes depending on the amount of HA produced at the single-cell level is required. Here, we evaluated for the first time the use of calcofluor white staining method combined with in vivo fluorescence confocal microscopy to quantify the heterogeneity in phenotypes of L. lactis cells engineered for HA production. From the microscopy image analysis, we found that the population harbours significant heterogeneity with respect to HA production and our novel approach successfully differentiates these phenotypes. Using the fluorescence intensity levels, first we were able to confidently differentiate cells not expressing HA (Host cells without HA genes for expression) from cells with genes for HA production (GJP2) and induced for expression, as there is a consistently two-fold higher level of expression in the GJP2 cells independently of the cell size. Further, this method revealed the occurrence of two different phenotypes in GJP2 cultures, one of a high-expression phenotype (40% of the population) and the other one of a low-expression (remaining 60% of the population), and it is the high expression phenotype that contributes to the increase in the HA expression of the GJP2 population compared with the host cells. Thus, it is essential to identify the extrinsic and intrinsic factors that can favour most of the cells in the population to switch and stabilise into the high-expression phenotype state in a bioreactor, for higher yield and possibly reduced heterogeneity of the product, such as polydispersity in chain lengths. For such optimisation studies, this in vivo method serves as a promising tool for rapid detection of phenotypes in the bioreactor samples under varying conditions, allowing fine tuning of the factors to stabilise high-expression phenotypes thereby maximizing the yield. Graphical Abstract done. Key Points Calcofluor staining successfully differentiated the phenotypes based on HA levels. This study revealed the occurrence of significant heterogeneity in HA expression. This method will aid for rapid optimization of factors for improved HA production.
Healing effects of a protein scaffold loaded with adipose-derived mesenchymal stem cells on radiation-induced vaginal injury in rats

Objectives Cervical cancer, the most common female cancer after breast cancer, is typically treated using radiotherapy. However, pelvic radiotherapy can cause irreversible damage to the vagina, seriously affecting patients’ quality of life. In this study, protein scaffolds loaded with rat adipose-derived mesenchymal stem cells (ADSCs) were implanted into irradiated tissue to assess their healing potential. Methods We established a rat model of radiation-induced vaginal injury. Complexes (consisting of protein scaffolds loaded with ADSCs) were implanted into injury sites. Histological analysis were used to assess regeneration of the vaginal epithelium. RNA sequencing was used to study the therapeutic mechanism of the complexes. Results The complexes promoted vaginal epithelial cell regeneration, vaginal tissue repair and improved vaginal stenosis and contracture. Compared with rats transplanted with ADSCs, rats transplanted with complexes achieved better therapeutic effects. Conclusions Protein scaffold-ADSC complexes had a beneficial therapeutic effect on radiation-induced vaginal injury in rats and may serve as the basis of a novel therapeutic approach for radiation dermatitis.
Conservation Genetics of the Endangered Del Mar Manzanita (Arctostaphylos glandulosa subsp. Crassifolia) Based On Rad Sequencing Data

Abstract Del Mar manzanita (Arctostaphylos glandulosa Eastw. subsp. crassifolia (Jeps.) P.V. Wells) is a federally listed endangered shrub found in San Diego County, California and Baja California, Mexico. This manzanita forms part of the imperiled southern maritime chaparral of southwestern California and adjacent Baja California, Mexico. Del Mar manzanita is problematic to identify because of morphological intergradation with other subspecies of A. glandulosa. Such intergradation could result from biological phenomena, such as gene flow among subspecies. Alternatively, it could be that the current circumscription of the Del Mar manzanita is not correct, and that the morphological characters used to diagnose this subspecies are inaccurate indicators of underlying genetics. This situation leads to problems for conservation planning, where accurate identification of individual plants is essential. Here, we used high-throughput sequencing of restriction-site associated DNA markers (RADseq) to develop single nucleotide polymorphism (SNP) data for a large sample of putative Del Mar manzanita, and a small sample of closely related subspecies of A. glandulosa. We analyzed genetic relationships using a total of 65,964 SNPs, with the aim of testing whether morphological traits used to identify Del Mar manzanita are an accurate reflection of underlying genetic patterns. We conclude that vegetative morphology is a poor predictor of genetic patterns, and that the current morphology-based circumscription of Del Mar manzanita is probably in need of some change. However, due to the limited sampling of A. glandulosa subspecies in this study, it is not possible to determine the taxonomic limits of Del Mar manzanita using our SNP data.
Patient‐reported outcomes in the setting of a randomized control trial on the efficacy of transcutaneous stimulation of the posterior tibial nerve compared to percutaneous stimulation in idiopathic overactive bladder syndrome

To compare the efficacy of transcutaneous tibial nerve stimulation (TTNS) with percutaneous tibial nerve stimulation (PTNS) regarding patient‐reported outcomes measures, specifically quality‐of‐life (QoL) improvement and patient's treatment benefit, on symptoms associated with overactive bladder (OAB).
Influence of dip-coating times towards oxygen separation performance

Several advantages possessed by carbon membrane such as can be easily processed, high gas separation performance and requires adequate amount of energy compared to the conventional separation process are the reasons it is deemed as the future media of separation. This study utilized PI blends and nanocrystalline cellulose (NCC) to prepare the tubular carbon membrane in order to investigate its fabrication. The effect of dip-coating duration (15, 30, 45, and 60 min) on physicochemical properties O2/N2 separation was determined. Carbonization was done at 800 °C with 3 °C/min rate of heating under argon gas flow (200 mL/min). Tests of pure gas permeation were conducted in order to study the transport mechanism of prepared carbon membrane at ambient temperature and 8 bar of feed pressure. Carbon membrane with O2 permeance of 29.92 ± 1.44 GPU and O2/N2 selectivity of 9.29 ± 2.54 were obtained after 45 min of dip coating.
Balancing competing life‐stage requirements in salmon habitat rehabilitation: between a rock and a hard place

Gravel augmentation is often applied to rivers and streams to rehabilitate salmonid spawning and incubation habitat. However, the effect of gravel size on salmon spawning utilization and embryo survival during incubation is not well understood. We conducted an experiment on a regulated and previously mined Northern California salmonid‐bearing stream in which different sized gravel (small, medium, and large) patches were placed into the stream's degraded spawning reach. We documented Oncorhynchus tshawytscha (Chinook salmon) spawning activity within the three gravel sizes for two seasons. In addition, we deployed Chinook salmon embryos into each gravel size patch and allowed them to incubate until estimated emergence time. Although all experimental gravel sizes were predicted to be within the spawning population's mobilization capabilities, model results indicated the probability of salmon building redds decreased as substrate size increased. Conversely, embryo survival increased as gravel size increased. A possible mechanism of disparate Chinook salmon embryo survival is provided by an observed decrease in embryo survival correlating with greater presence of embryo predators (leeches), which are associated with smaller gravel. Our results indicate a parent‐offspring conflict in optimal spawning gravel size for Chinook salmon, and suggest that an intermediate gravel size would maximize overall reproductive success across both spawning and incubation life stages.
Effects of Doping Concentration and Annealing Temperature on Indium Doped Zinc Oxide Particles Prepared via Sol-Gel Method:

Doping of indium in zinc oxide (ZnO) is one of the means to increase its electrical conductivity. This study focuses on investigating the effects of indium doping concentration (In/Zn = 3%, 5% and 7%) and annealing temperature (200°C, 300°C and 450°C) on the electrical conductivity, structural, morphological and elemental properties of the indium doped zinc oxide (IZO) particles. The synthesis of IZO particles was carried out by a simple sol-gel method where sol-gel was evaporated to xerogel, heat treated and milled to form solid particles. The particles were characterized by four-point probe, X-ray diffraction (XRD), Fourier transform infrared (FTIR) and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDX). The results obtained demonstrate an impressive increase of electrical conductivity by one order of magnitude at 5% of indium doping compared to the pristine zinc oxide (ZnO) as a result of cumulative charge carriers. Besides, an increase of annealing temperature also shows a positive effect on the electrical conductivity. XRD results show distinctive changes on crystal structure of polycrystalline wurtzite structure and its crystallite size with the change in parameters. FTIR results indicate the effects of both parameters by the presence and elimination of peaks designated for IZO functional group. The SEM-EDX analysis reveals the microstructure morphology at different parameters and validates the existence of each element according to doping concentration.
Factors Influencing Lunar Surface Analysis Using X-Ray Fluorescence Spectrography

Introduction: In recent years there have been several X-ray fluorescence spectography instruments flown on lunar missions, and in the near future there will be more, both on missions to the Moon and beyond, for instance to Mercury. An X-ray spectrometer instrument can remotely detect the mineralogy of the surface of atmosphere-less terrestrial bodies by recording the X-ray fluorescence caused when the surface is bombarded by solar X-ray events. The Chandrayaan-1 X-ray Spectrometer (C1XS), which flew on ISRO’s Chandrayaan-1 mission in 2008, was one such instrument [1]. Remote sensing with X-ray spectrometers samples only the upper few microns of the surface [2]. Clearly any surface feature or process that alters the elemental abundances of the upper surface will affect the signal received by such instruments, and may disguise the bulk mineralogy under investigation. More quantitative understanding of these effects will be useful for analysing C1XS data, and for planning similar up-coming missions. We have investigated two such sources of signal contamination: crater rays and surface/atmospheric volatiles. Lunar crater rays rank amongst the brightest and most impressive features of the Moon. A ray will typically consist of a long, bright feature stretching out from a source crater [3]. Rays are thought to consist of several types – immaturity rays, where the brightness is due to the relative youth of the overlying ray material; compositional rays, where the mineralogical content of the ray is different to the underlying surface; and combination rays, which are formed by a mixture of the two effects.
Phytochemical analysis, antimicrobial and antioxidant activity evaluations of fruit of Artocarpus heterophyllus Lam

1Department of Botany and Research Centre, Nesamony Memorial Christian College, Marthandam, Kanyakumari District, Tamil Nadu-629165, India 2Biovent, KU-TBSC Start up, Department of Biotechnology, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala–695 581, India 3Department of Chemistry, Arba Minch University, Abaya Campus, Arba Minch, PB No. 21, Ethiopia 4Department of Biotechnology and Research, K. V. M. College of Science and Technology, Kokkothamangalam PO, Cherthala-688583, Alappuzha District, Kerala State, India
Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e

Numerous gene expression and stress adaptation responses in L. monocytogenes are regulated through alternative sigma factors σB and σL. Stress response phenotypes and transcriptomes were compared between L. monocytogenes EGD-e and its ΔsigB and ΔsigBL mutants. Targeted growth phenotypic analysis revealed that the ΔsigB and ΔsigBL mutants are impaired during growth under cold and organic-acid stress conditions. Phenotypic microarrays revealed increased sensitivity in both mutants to various antimicrobial compounds. Genes de-regulated in these two mutants were identified by genome-wide transcriptome analysis during exponential growth in BHI. The ΔsigB and ΔsigBL strains repressed 198 and 254 genes, respectively, compared to the parent EGD-e strain at 3 °C, whereas 86 and 139 genes, respectively, were repressed in these mutants during growth at 37 °C. Genes repressed in these mutants are involved in various cellular functions including transcription regulation, energy metabolism and nutrient transport functions, and viral-associated processes. Exposure to cold stress induced a significant increase in σB and σL co-dependent genes of L. monocytogenes EGD-e since most (62%) of the down-regulated genes uncovered at 3 °C were detected in the ΔsigBL double-deletion mutant but not in ΔsigB or ΔsigL single-deletion mutants. Overall, the current study provides an expanded insight into σB and σL phenotypic roles and functional interactions in L. monocytogenes. Besides previously known σB- and σL-dependent genes, the transcriptomes defined in ΔsigB and ΔsigBL mutants reveal several new genes that are positively regulated by σB alone, as well as those co-regulated through σB- and σL-dependent mechanisms during L. monocytogenes growth under optimal and cold-stress temperature conditions.
A study of intra articular platelet rich Plasma therapy in the treatment of knee Osteoarthritis

Introduction: Osteoarthritis (OA) represents a failure of the di-arthrodial, synovial lined joint. Among the elderly, knee Osteoarthritis is the leading cause of chronic disability [1]. Because of the increased lifespan and obesity the prevalence of osteoarthritis is in the rise in India. Aim of the Study: Whether platelet rich plasma is useful in OAknee or not. Objectives: To evaluate the role of Autologous Platelet Rich plasma (APRP) in the treatment of patients presenting with primary osteoarthritis and to analyze whether it could be a cost effective disease modifying measure. Materials and Methods: Total 100 OA Knee cases are selected from the Katuri Medical College and Hospital, randomly. First 50 were given A PRP injection to the OA Knee, Next 50 were given normal saline. Platelet-Rich Plasma: Platelets are cytoplasmic fragments of megakaryocytes, that are formed in the marrow [26] and are approximately 2 μm in diameter. They contain more than thirty bioactive proteins, of which many of them have a fundamental role in hemostasis or in tissue healing [28]. Fundamental protein growth factors which are actively secreted by platelets will initiate all the wound healing process [29] PRP includes three proteins in blood which is known to act as cell adhesion molecules: Fibrin, fibronectin and vitronectin [30]. Discussion: Osteoarthritis is a disorder of synovial joints characterized by focal loss of hyaline cartilage with proliferation of new bone and remodeling of joint contour, mainly due to uncoupling of balance between cartilage regeneration and degeneration. Osteoarthritis is a dynamic repair process of synovial joints that may be triggered a variety of insults. We in our study had randomly chosen 100 patients with classic findings of Osteoarthritis and divided them in to two groups. Both the groups were comparable on baseline characteristics of age, height, weight, BMI, pre injection WOMAC score. Fifty of these patients were administered an intra articular injection of Platelet Rich Plasma and other fifty received Normal Saline. The Efficacy of Platelet Rich Plasma in reducing pain, stiffness and physical function were assessed and scored on WOMAC index for both study and control group. The Results were analyzed using unpaired ‘t’ test and chisquare test. Age distribution revealed mean age in group I to be 53.14 and the mean age in Group II was 53.68. Outcome Analysis: The study group and the control group are advised to follow up at 6 weeks, 3 months and 6 months. Outcome analysis for the efficacy was done for reduction in pain, reduction in stiffness and improvement in physical function using WOMAC scale. The Patients were also assessed for reduction in pain using Visual analog scale both at pre injection and at 6 months post injection. Conclusion: Our study has thrown up an interesting choice of treatment modality using Platelet Rich Plasma in the treatment of Knee Osteoarthritis and it has proved efficacious in the observation period of six months.
Genetic diversity of groundnut rhizosphere antagonistic bacteria and biological control of groundnut wilted diseases in central Vietnam

Stem rot of groundnut caused by Sclerotium rolfsii, seriously damages groundnut production in central Vietnam. Biological control is a promising strategy for sustainable groundnut cultivation. In this study, indigenous bacteria were isolated from the rhizosphere of groundnut and tested for fungal inhibition against S. rolfsii in vitro and disease control under net house condition. Genetic diversity of isolated bacterial population was evaluated by BOX-PCR and 16S rDNA sequences. Bacterial strains that showed high disease control in net house were evaluated under natural conditions in farmer fields. The antifungal mechanism of the best bacterial strain was identified. Results of the study showed that the antagonistic bacterial population in groundnut rhizosphere is separated in three bacterial genera including Bacillus, Pseudomonas and Burkholderia. One bacterial strain which produces 2,4-DAPG reduced stem rot of groundnut caused by S. rolfsii and increased yield from 20.3 to 26.3% compared to the control.
Comparison of the Performance of Climbing Perch (Anabas testudineus Bloch) Filial 2 Fry and Natural Fry Treated in Acidic Swamp Waters, Jejangkit Village, South Kalimantan

Ansyari F, Slamat S. 2020. Comparison of the performance of climbing perch (Anabas testudineus Bloch) filial 2 fry and natural fry treated in acidic swamp waters, Jejangkit Village, South Kalimantan. Jurnal Lahan Suboptimal: Journal of Suboptimal Lands 9(1): 23-30.The aim of the study was to compare the performance (survival rate, growth and feed conversion) of climbing perch fish fry Filial 2 (F2) which has superior characteristics with natural fry that are culture in sour swamp waters. The study was carried out in swamp waters, Jejangkit Village, Barito Kuala Regency, South Kalimantan for 6 months (January to June 2019). This study compared fish performances generated from F2 fry of nature. Fishes were cultured in net (4 m x 2 m x 1 m) with the same stocking density of 100 fishes/m2 . The results showed that the survival rate of natural fry was 86.6% higher than that of F2 75.3%, but the relative growth of natural fry was 2,325% lower thanÂ F2 3,060% and feed conversion natural fry was 3.03 less efficient than F2 fry 2.62. It was concluded that the performance of F2 fry was better than natural fry, when maintained in acidic swamp waters.
Costs and effectiveness of damage management of an overabundant species (Sus scrofa) using aerial gunning

Abstract Context. Management of overabundant or invasive species is a constant challenge because resources for management are always limited and relationships between management costs, population density and damage costs are complex and difficult to predict. Metrics of management success are often based on simple measures, such as counts, which may not be indicative of impacts on damage reduction or cost-effectiveness under different management plans. Aims. The aims of this study were to evaluate the effectiveness of aerial gunning for the management of wild pigs (Sus scrofa), and to evaluate how cost-effectiveness would vary under different relationships between levels of damage and densities of wild pigs. Methods. Repeated reduction events were conducted by aerial gunning on three consecutive days at three study sites. Using a removal model, the proportion of the population removed by each flight was estimated and population modelling was used to show the time it would take for a population to recover. Three possible damage–density relationships were then used to show the level of damage reduction (metric of success) from different management intensities and levels of population recovery, and these relationships were expressed in terms of total costs (including both damage and management costs). Key results. Populations were typically reduced by ∼31% for the first flight, ∼56% after two flights and ∼67% after three flights. When the damage relationship suggests high damage even at low densities, the impact of one, two or three flights would represent a reduction in damage of 2%, 19% and 60% respectively after 1 year. Different damage relationships may show considerable damage reduction after only one flight. Removal rates varied by habitat (0.05 per hour in open habitats compared with 0.03 in shrubby habitats) and gunning team (0.03 versus 0.05). Conclusions. Monitoring the efficacy of management provides critical guidance and justification for control activities. The efficacy of different management strategies is dependent on the damage–density relationship and needs further study for effective evaluation of damage reduction efforts. Implications. It is critically important to concurrently monitor density and damage impacts to justify resource needs and facilitate planning to achieve a desired damage reduction goal.