Evidence for tropospheric ozone effects on rice production in Bangladesh

Although Bangladesh is known to be burdened with elevated tropospheric ozone levels, little is known about its effects on food security. We conducted field experiments in four highly polluted rice growing environments of Bangladesh in three cropping seasons (2020-2022), in which we grew 20 different rice varieties with or without application of the ozone protectant ethylene diurea (EDU). The average daytime ozone concentrations at the study sites during the rice growing seasons ranged from 53 ppb to 84 ppb, with the lowest concentrations occurring in the year 2020. EDU increased rice grain yields significantly by an average of 10.4 % across all seasons and locations, indicating that plants were stressed under ambient ozone concentrations. EDU was effective in distinguishing ozone-tolerant from ozone-sensitive varieties, in which yield increased by up to 21 %. Likewise, the EDU treatment positively affected vegetation indices representing chlorophyll (NDVI), the chorophyll:carotenoid ratio (Lic2), and pigments of the xanthophyll cycle (PRI). Stomatal conductance was increased significantly by an average of around 10 % among all varieties when plants were treated with EDU. In all physiological traits, significant genotype by treatment interactions occurred, indicating that different varieties varied in their responses to ozone stress. Our study demonstrates that rice production in Bangladesh is severely affected by tropospheric ozone, and calls for the breeding of tolerant rice varieties as well as mitigation measures to reduce air pollution.

Effectiveness of "Physician Prompt Clinical Decision Criteria" in Weaning Outcome Prediction for Neurocritical Patients

Endotracheal intubation and invasive mechanical ventilation are fundamental components for the resuscitation of neurocritically ill patients to achieve various goals which include ensuring the protection of the airway, participating in tissue oxygen delivery and indirectly modulating cerebral vascular reactivity. The neurocritical patients demand special attention to their systemic involvement regarding weaning. Physician prompt clinical decision criteria (PPC) can play a better role in weaning of such patients. The aim of this study was to evaluate the effectiveness of 'Physician prompt clinical decision criteria' for successful weaning in neurocritical patients. This prospective observational study was conducted in the ICU, Department of Anaesthesia, Analgesia, Palliative & Intensive Care Medicine, Dhaka Medical College Hospital (DMCH), Dhaka, Bangladesh from March 2018 to April 2020. In total 100 neurocritical patients who fulfilled the inclusion criteria were taken as samples by informed written consent. The outcome was observed as successful weaning or as failed weaning. Finally, the existence of Standard extubation criteria (SEC) was compared with Physician prompt clinical decision criteria (PPC). Weaning was succeeded in 80.0% of patients and failed in 20.0% according to the Standard extubation criteria (SEC) while weaning was succeeded in 85.7% of patients and failed in 14.28% according to the Physician prompt clinical decision criteria (PPC). There were some differences in results but no significant differences were observed statistically between the groups in predicting the weaning outcome. Physician prompt clinical decision criteria were found to be 75.0% sensitive and specificity was 50.0%. Positive predictive value for Physician prompt clinical decision criteria was 85.70% with a Positive likelihood ratio for these criteria was 1.5 times. So, according to the study findings, accuracy of Physician prompt clinical decision criteria was 70.0%. According to the findings of this current study we can conclude that Physician prompt clinical decision criteria are an effective weaning readiness predictor in neurocritical patients.

Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions

Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.

Ectopic expression of Vigna radiata's vacuolar Na+/H+ antiporter gene (VrNHX1) in indica rice (Oryza sativa L.)

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Successful Agrobacterium-mediated transformation of indica Dhan28 and BRRI Dhan29

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Ectopic expression of the Na+/H+ exchanger 1 (VrNHX1) from Vigna radiata L. Wilczek in indica rice improves salinity tolerance.

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Under 150 mM NaCl salinity stress, transgenic lines performed significantly better than wild type.

It is essential to develop high salt-tolerant rice varieties in order to cultivate the salt-affected lands. In this study, Na⁺/H⁺ exchanger 1 (NHX1) gene isolated from Vigna radiata L. Wilczek was transferred in Bangladesh Rice Research Institute (BRRI) developed two indica rice genotypes BRRI Dhan28 and BRRI Dhan29 using in-planta approach for improvement of salinity tolerance. Embryonic axes of matured dehusked rice seeds were injured and co-cultivated with Agrobacterium strain harboring VrNHX1 gene and finally regenerated. GUS histochemical assay and PCR amplification of GUS-a and VrNHX1 were performed to confirm the transformation. Expression confirmation was done by semi-quantitative RT-PCR. Under salinity stress, transgenic lines showed higher chlorophyll, relative water content and decreased electrolyte leakage, proline content, lipid peroxidation level, and catalase enzyme activity which represent the better physiology than control plants. Moreover, under salinity stress (150 mM), transgenic lines exhibited superior growth and salt tolerant than non-transgenic plants.

Addition of three new angiospermic taxa to the flora of Bangladesh

During updating the plant holding database of the botanical garden, Bangladesh Agricultural University, the authors identified three species of the family Commelinaceae namely, Callisia fragrans (Lindl.) Woodson, Murdannia gigantea (Vahl) G.Brückn., and Tradescantia sillamontana Matuda as new records to the flora of Bangladesh. This paper provides a comprehensive description and colour photographs of these species from Bangladesh. 

Mitochondrial ion channels in aging and related diseases

Transport of materials and information across cellular boundaries, such as plasma, mitochondrial and nuclear membranes, happens mainly through varieties of ion channels and pumps. Various biophysical and biochemical processes play vital roles. The underlying mechanisms and associated phenomenological lipid membrane transports are linked directly or indirectly to the cell health condition. Mitochondrial membranes (mitochondrial outer membrane (MOM) and mitochondrial inner membrane (MIM)) host crucial cellular processes. Their malfunction is often found responsible for the rise of cell-originated diseases, including cancer, Alzheimer's, neurodegenerative disease, etc. A large number of ion channels active across MOM and MIM are known to belong to vital cell-based structures found to be linked directly to cellular signaling. Hence their malfunctions are often found to contribute to abnormalities in intracellular communication, which may even be associated with the rise of various diseases. In this article, the aim is to pinpoint ion channels that are directly or indirectly linked to especially aging and related abnormalities in health conditions. An attempt has been made to address the natural structures of these channels, their mutated conditions, and the ways we may cause interventions in their malfunctioning. The malfunction of ion channel subunits, including especially various proteins, involved directly in channel formation and/or indirectly in channel stabilization, leads to the rise of various channel-specific diseases, which are known as channelopathies. Channelopathies in aging will be discussed briefly. This mini-review may be found as an important reference for drug discovery scientists dealing with aging-related diseases.

Artificial Intelligence, Machine Learning and Deep Learning in Ion Channel Bioinformatics

Ion channels are linked to important cellular processes. For more than half a century, we have been learning various structural and functional aspects of ion channels using biological, physiological, biochemical, and biophysical principles and techniques. In recent days, bioinformaticians and biophysicists having the necessary expertise and interests in computer science techniques including versatile algorithms have started covering a multitude of physiological aspects including especially evolution, mutations, and genomics of functional channels and channel subunits. In these focused research areas, the use of artificial intelligence (AI), machine learning (ML), and deep learning (DL) algorithms and associated models have been found very popular. With the help of available articles and information, this review provide an introduction to this novel research trend. Ion channel understanding is usually made considering the structural and functional perspectives, gating mechanisms, transport properties, channel protein mutations, etc. Focused research on ion channels and related findings over many decades accumulated huge data which may be utilized in a specialized scientific manner to fast conclude pinpointed aspects of channels. AI, ML, and DL techniques and models may appear as helping tools. This review aims at explaining the ways we may use the bioinformatics techniques and thus draw a few lines across the avenue to let the ion channel features appear clearer.

Multidisciplinary Team Effort Results in Better Outcomes in Critically Ill Obstetric Patients Admitted in ICU

Management of critically ill obstetric patients is a great challenge for the ICU team. The safety of both mother and fetus are of real concerns. Teamwork is essential for better outcome in obstetric patients in the ICU. A 26 years old female was admitted in Dhaka Medical College Hospital, Dhaka, Bangladesh on 18 August 2019 with 7 months pregnancy with brain tumor (later diagnosed as Gliosarcoma) and was managed surgically by left temporal craniotomy with excision of the tumor. The patient was shifted to the ICU due to repeated convulsions and need mechanical ventilator support. Later on, she was suffering from sepsis with pseudomonas in blood culture, grade IV pressure ulcer and electrolyte imbalance and needed tracheostomy for airway management. On 34th weeks of her pregnancy she developed antepartum hemorrhage with respiratory distress. Emergency LUCS was done and she delivered a LBW baby who was managed in NICU. Mother was managed in the ICU and later on both mother and child were discharge with good conditions. Multidisciplinary team work is vital for better management of critically ill obstetric patients.

Assessing impacts of COVID-19 on aquatic food system and small-scale fisheries in Bangladesh

COVID-19 is now a major global health crisis, can lead to severe food crisis unless proper measures are taken. Though a number of scientific studies have addressed the possible impacts of COVID-19 in Bangladesh on variety of issues, problems and food crises associated with aquatic resources and communities are missing. Therefore, this study aimed at bridging the gap in the existing situation and challenges of COVID-19 by linking its impact on aquatic food sector and small-scale fisheries with dependent population. The study was conducted based on secondary data analysis and primary fieldwork. Secondary data focused on COVID-19 overview and number of confirmed, recovered and death cases in Bangladesh; at the same time its connection with small-scale fisheries, aquatic food production, demand and supply was analyzed. Community perceptions were elicited to present how the changes felt and how they affected aquatic food system and small-scale fisheries and found devastating impact. Sudden illness, reduced income, complication to start production and input collection, labor crisis, transportation abstraction, complexity in food supply, weak value chain, low consumer demand, rising commodity prices, creditor's pressure were identified as the primary affecting drivers. Dependent people felt the measures taken by the Government should be based on protecting both the health and food security. Scope of alternative income generating opportunities, rationing system, training and motivational program could improve the situation. The study provides insight into policies adopted by the policy makers to mitigate the effects of the pandemic on aquatic food sector and small-scale fisheries.

The Antimicrobial Peptide Gramicidin S Enhances Membrane Adsorption and Ion Pore Formation Potency of Chemotherapy Drugs in Lipid Bilayers

We recently published two novel findings where we found the chemotherapy drugs (CDs) thiocolchicoside (TCC) and taxol to induce toroidal type ion pores and the antimicrobial peptide gramicidin S (GS) to induce transient defects in model membranes. Both CD pores and GS defects were induced under the influence of an applied transmembrane potential (≈100 mV), which was inspected using the electrophysiology record of membrane currents (ERMCs). In this article, I address the regulation of the membrane adsorption and pore formation of CDs due to GS-induced possible alterations of lipid bilayer physical properties. In ERMCs, low micromolar (≥1 μM) GS concentrations in the aqueous phase were found to cause an induction of defects in lipid bilayers, but nanomolar (nM) concentration GS did nothing. For the binary presence of CDs and GS in the membrane-bathing aqueous phase, the TCC pore formation potency is found to increase considerably due to nM concentration GS in buffer. This novel result resembles our recently reported finding that due to the binary aqueous presence of two AMPs (gramicidin A or alamethicin and GS), the pore or defect-forming potency of either AMP increases considerably. To reveal the underlying molecular mechanisms, the influence of GS (0-400 nM) on the quantitative liposome (membrane) adsorption of CD molecules, colchicine and TCC, was tested. I used the recently patented direct detection method, which helps detect the membrane active agents directly at the membrane in the mole fraction relative to its concentrations in aqueous phase. We find that GS, at concentrations known to do nothing to the lipid bilayer electrical barrier properties in ERMCs, increases the membrane adsorption (membrane uptake) of CDs considerably. This phenomenological finding along with the GS effects on CD-induced membrane conductance increase helps predict an important conclusion. The binary presence of AMPs alongside CDs in the lipid membrane vicinity may work toward enhancing the physical adsorption and pore formation potency of CDs in lipid bilayers. This may help understand why CDs cause considerable cytotoxicity.

Genetic dissection of bread wheat diversity and identification of adaptive loci in response to elevated tropospheric ozone

Rising tropospheric ozone affects the performance of important cereal crops thus threatening global food security. In this study, genetic variation of wheat regarding its physiological and yield responses to ozone was explored by exposing a diversity panel of 150 wheat genotypes to elevated ozone and control conditions throughout the growing season. Differential responses to ozone were observed for foliar symptom formation quantified as leaf bronzing score (LBS), vegetation indices and yield components. Vegetation indices representing the carotenoid to chlorophyll pigment ratio (such as Lic2) were particularly ozone-responsive and were thus considered suitable for the non-invasive diagnosing of ozone stress. Genetic variation in ozone-responsive traits was dissected by a genome-wide association study (GWAS). Significant marker-trait associations were identified for LBS on chromosome 5A and for vegetation indices (NDVI and Lic2) on chromosomes 6B and 6D. Analysis of linkage disequilibrium (LD) in these chromosomal regions revealed distinct LD blocks containing genes with a putative function in plant redox biology such as cytochrome P450 proteins and peroxidases. This study gives novel insight into the natural genetic variation in wheat ozone response, and lays the foundation for the molecular breeding of tolerant wheat varieties.

Dataset on interactions of membrane active agents with lipid bilayers

We address drug interactions with lipids using in silico simulations and in vitro experiments. The data article provides extended explanations on molecular mechanisms behind membrane action of membrane-active agents (MAAs): antimicrobial peptides and chemotherapy drugs. Complete interpretation of the data is found in the associated original article ‘charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers’ [1]. Data on molecular dynamic simulations of the drug lipid complexes are provided. Additional data and information are provided here to explain the connectivity among various information and techniques used for understanding of the membrane action and/or binding of MAAs including aptamers. Brief explanation has been provided on the possibility of achieving a converted triangle from newly discovered quadrangle, sides of which explain four different phenomena: ‘membrane effects’, ‘detection and quantification’, ‘origin of energetics’ and ‘structure stability’ while drug effects occur. Triangle or quadrangle corners represent various techniques that were applied.

The Influence of Surface Topography on the Weak Ground Shaking in Kathmandu Valley during the 2015 Gorkha Earthquake, Nepal

It remains elusive why there was only weak and limited ground shaking in Kathmandu valley during the 25 April 2015 Mw 7.8 Gorkha, Nepal, earthquake. Our spectral element numerical simulations show that, during this earthquake, surface topography restricted the propagation of seismic energy into the valley. The mountains diverted the incoming seismic wave mostly to the eastern and western margins of the valley. As a result, we find de-amplification of peak ground displacement in most of the valley interior. Modeling of alternative earthquake scenarios of the same magnitude occurring at different locations shows that these will affect the Kathmandu valley much more strongly, up to 2-3 times more, than the 2015 Gorkha earthquake did. This indicates that surface topography contributed to the reduced seismic shaking for this specific earthquake and lessened the earthquake impact within the valley.

Shoot sodium exclusion in salt stressed barley (Hordeum vulgare L.) is determined by allele specific increased expression of HKT1;5

High affinity potassium transporters (HKT) are recognized as important genes for crop salt tolerance improvement. In this study, we investigated HvHKT1;5 as a candidate gene for a previously discovered quantitative trait locus that controls shoot Na⁺ and Na⁺/K⁺ ratio in salt-stressed barley lines on a hydroponic system. Two major haplotype groups could be distinguished for this gene in a barley collection of 95 genotypes based on the presence of three intronic insertions; a designated haplotype group A (HGA, same as reference sequence) and haplotype group B (HGB, with insertions). HGB was associated with a much stronger root expression of HKT1;5 compared to HGA, and consequently higher K⁺ and lower Na⁺ and Cl^- concentrations and a lower Na⁺/K⁺ ratio in the shoots three weeks after exposure to 200 mM NaCl. Our experimental results suggest that allelic variation in the promoter region of the HGB gene is linked to the three insertions may be responsible for the observed increase in expression of HvHKT1;5 alleles after one week of salt stress induction. This study shows that in barley - similar to wheat and rice - HKT1;5 is an important contributor to natural variation in shoot Na⁺ exclusion.

Enhanced ascorbate level improves multi-stress tolerance in a widely grown indica rice variety without compromising its agronomic characteristics

A biotechnological approach was adopted for increasing foliar ascorbate levels as a strategy to adapt a widely grown high yielding rice variety to multiple abiotic stresses. The variety IR64 (Oryza sativa L. ssp. indica) was engineered to express the ascorbate biosynthesis gene GDP-L-galactose phosphorylase (AcGGP) from kiwifruit (Actinidia chinensis Planch.) under the control of a leaf-specific promoter of the Leaf Panicle 2 (LP2) gene. Transgene expression increased foliar ascorbate levels up to >2.5 fold but did not lead to any changes in morphological traits (seed yield, sterility rate, grain weight, and biomass) in non-stress conditions. We then hypothesized that enhanced foliar ascorbate would confer multi-stress tolerance. Indeed transgenic lines were more tolerant to salinity in terms of lipid peroxidation and foliar symptoms, and to drought in terms of lipid peroxidation and post-drought recovery (number of dead leaves). A significantly better performance in ozone stress was seen only when ozone coincided with salinity. However, no differences between transgenic lines and wild types occurred when plants were subjected to toxicities in redox-active transition metals, i.e. iron and manganese, although plants showed clear symptoms of oxidative stress. Moreover, no differential response to zinc deficiency was observed, because the background genotype IR64 was not sensitive to this stress. Taken together, our study helps to identify stress conditions that can be mitigated by enhancing foliar ascorbate levels, and therefore facilitates an adaptive breeding approach for multiple stresses that would not imply any yield penalty.

Climate change and human health linkages in the context of globalization: An overview from global to southwestern coastal region of Bangladesh

This article attempts to analyze the main impacts of climate change on public health starting with global and going through local by analyzing coastal communities in the area of influence of Sundarbans, located in southwestern coastal region of Bangladesh. In dealing with paramount health problems caused by climate change, we discuss what are the major challenges faced by different actors. From the opinion of globalization and world system theory it will be argued that developing countries are facing major defiance in terms of mitigation and adaptation, including human health problems. Those living in developing world, as the case of Bangladesh, responsible for the lowest contributions to climate change, are already suffering the most. This paper is based on bibliographical and statistical review, and uses primary data collected from field and secondary from publications, books, scientific journals, international reports. In this paper we also focused that poor countries shall not be liable for the damages caused by carbon emissions already trapped into atmosphere, a historic problem caused by developed world, so we expect that multi-governance platforms should make mutual efforts to promote health in partnership with local institutions in order to solve the climatic crisis.

Ethylenediurea (EDU) mitigates the negative effects of ozone in rice: Insights into its mode of action

Monitoring of ozone damage to crops plays an increasingly important role for the food security of many developing countries. Ethylenediurea (EDU) could be a tool to assess ozone damage to vegetation on field scale, but its physiological mode of action remains unclear. This study investigated mechanisms underlying the ozone-protection effect of EDU in controlled chamber experiments. Ozone sensitive and tolerant rice genotypes were exposed to ozone (108 ppb, 7 hr day^-1 ) and control conditions. EDU alleviated ozone effects on plant morphology, foliar symptoms, lipid peroxidation, and photosynthetic parameters in sensitive genotypes. Transcriptome profiling by RNA sequencing revealed that thousands of genes responded to ozone in a sensitive variety, but almost none responded to EDU. Significant interactions between ozone and EDU application occurred mostly in ozone responsive genes, in which up-regulation was mitigated by EDU application. Further experiments documented ozone degrading properties of EDU, as well as EDU deposits on leaf surfaces possibly related to surface protection. EDU application did not mitigate the reaction of plants to other abiotic stresses, including iron toxicity, zinc deficiency, and salinity. This study provided evidence that EDU is a surface protectant that specifically mitigates ozone stress without interfering directly with the plants' stress response systems.

Diagnosing ozone stress and differential tolerance in rice (Oryza sativa L.) with ethylenediurea (EDU)

Rising tropospheric ozone concentrations in Asia necessitate the breeding of adapted rice varieties to ensure food security. However, breeding requires field-based evaluation of ample plant material, which can be technically challenging or very costly when using ozone fumigation facilities. The chemical ethylenediurea (EDU) has been proposed for estimating the effects of ozone in large-scale field applications, but controlled experiments investigating constitutive effects on rice or its suitability to detect genotypic differences in ozone tolerance are missing. This study comprised a controlled open top chamber experiment with four treatments (i) control (average ozone concentration 16 ppb), (ii) control with EDU application, (iii) ozone stress (average 77 ppb for 7 h daily throughout the season), and (iv) ozone stress with EDU application. Three contrasting rice genotypes were tested, i.e. the tolerant line L81 and the sensitive Nipponbare and BR28. The ozone treatment had significant negative effects on plant growth (height and tillering), stomatal conductance, SPAD value, spectral reflectance indices such as the normalized difference vegetation index (NDVI), lipid peroxidation, as well as biomass and grain yields. These negative effects were more pronounced in the a priori sensitive varieties, especially the widely grown Bangladeshi variety BR28, which showed grain yield reductions by 37 percent. EDU application had almost no effects on plants in the absence of ozone, but partly mitigated ozone effects on foliar symptoms, lipid peroxidation, SPAD value, stomatal conductance, several spectral reflectance parameters, panicle number, grain yield, and spikelet sterility. EDU responses were more pronounced in sensitive genotypes than in the tolerant L81. In conclusion, EDU had no constitutive effects on rice and partly offset negative ozone effects, especially in sensitive varieties. It can thus be used to diagnose ozone damage in field grown rice and for distinguishing tolerant (less EDU-responsive) and sensitive (more EDU-responsive) genotypes.

Fournier’s Gangrene: Approaches to the Diagnosis and Treatment

Background: Fournier’s gangrene is a rare, rapidly progressive, necrotizing fasciitis of the external genitalia and perineum.Objective: The main aim of this study was to observe comprehensively the disease profile of Fournier’s gangrene, with a specific intent to observe the proportion of patient presenting with Fournier’s gangrene.Materials and method: This cross sectional study was done in Sir Salimullah Medical College & Mitford Hospital, Dhaka, Bangladesh. By purposive sampling from the admitted patients of department of Surgery 22 patients were finalized according to the eligibility criteria. Patients were thoroughly evaluated and managed and all relevant data were recorded. Data were managed, edited and plotted in tabular and figure form. Data analysis was done by chi square test. p value was significant at <0.05.Results: The mean ±SD age of the patients was 43.9±14.82 years. Among the study subjects 68.2% showed insidious onset whereas remaining showed abrupt onset. Both cutaneous and anorectal factors claimed the highest (36.4%) of etiology. Pain and Oedema were the prime manifestation. In 59% cases testes were not exposed. In 36.4% cases only scrotum was involved whereas in 22.7% cases both scrotum and perineum were involved. After provision of aggressive treatment in 72.7% cases no complication was observed. During treatment 9.1% subjects expired.Conclusion: Elderly and low economic profile people are frequently affected with Fournier’s gangrene. To reduce the significant morbidity and mortality aggressive medical and surgical management is mandatory.Delta Med Col J. Jul 2017 5(2): 68-75

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice

Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to changes of the function of the communities.

Regulation of channel function due to physical energetic coupling with a lipid bilayer

Regulation of membrane protein functions due to hydrophobic coupling with a lipid bilayer has been investigated. An energy formula describing interactions between lipid bilayer and integral ion channels with different structures, which is based on the screened Coulomb interaction approximation, has been developed. Here the interaction energy is represented as being due to charge-based interactions between channel and lipid bilayer. The hydrophobic bilayer thickness channel length mismatch is found to induce channel destabilization exponentially while negative lipid curvature linearly. Experimental parameters related to channel dynamics are consistent with theoretical predictions. To measure comparable energy parameters directly in the system and to elucidate the mechanism at an atomistic level we performed molecular dynamics (MD) simulations of the ion channel forming peptide-lipid complexes. MD simulations indicate that peptides and lipids experience electrostatic and van der Waals interactions for short period of time when found within each other's proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides (in ion channel) and lipids (in lipid bilayer) due to mainly their charge properties. The results of in silico MD studies taken together with experimental observable parameters and theoretical energetic predictions suggest that the peptides induce ion channels inside lipid membranes due to peptide-lipid physical interactions. This study provides a new insight helping better understand of the underlying mechanisms of membrane protein functions in cell membrane leading to important biological implications.

A computationally designed DNA aptamer template with specific binding to phosphatidylserine

The phospholipid phosphatidylserine (PS) is an early marker exploited for detecting apoptosis (PS externalization in the cell membrane bilayer) and one factor that is associated with increased amyloid plaque deposition in transmissible spongiform encephalopathies (TSEs). PS can therefore be considered as a promising target for diagnosis or treatment of diseases. Aptamers (short nucleic acid sequences) are a particularly attractive class of materials among those currently considered for targeting PS. Here we applied an entropy based seed-and-grow strategy to design a DNA aptamer template to bind specifically to PS. The binding properties of designed aptamers were investigated computationally and experimentally. The studies identify the sequence, 5'-AAAGAC-3', as the preferred template for further modifications and studies toward its practical implementations.

Variation in antioxidant attributes at three ripening stages of guava (Psidium guajava L.) fruit from different geographical regions of Pakistan

The present investigation was carried out to appraise the levels of total phenols and vitamin C as well as antioxidant potential at three different ripening stages (un-ripe, semi-ripe and fully-ripe) of guava (Psidium guajava L.) fruit collected from three different geographical regions of Pakistan (Islamabad, Faisalabad and Bhakkar). The antioxidant potential of guava fruit extracts was assessed by means of different in-vitro antioxidant assays, namely inhibition of peroxidation in linoleic acid system, reducing power and radical scavenging capability. Overall, fruit at the un-ripe stage (G1) exhibited the highest levels of TPC, TFC, reducing power and DPPH radical scavenging activity, followed by the semi-ripe (G2) and fully-ripe (G3) stages. On the other hand, vitamin C content increased as the fruit maturity progressed, with highest value seen at the fully-ripe stage (G3) followed by the semi-ripe (G2) and un-ripe stage (G1). The concentration of vitamin C in fruits varied as: Faisalabad (136.4–247.9 mg 100 g⁻¹), Islamabad (89.7–149.7 mg 100 g⁻¹) and Bhakkar (73.1–129.5 mg 100 g⁻¹). The results showed that different stages of maturation and geographical locations had profound effects on the antioxidant activity and vitamin C contents of guava fruit.

Risk Factors of Neonatal Mortality in Bangladesh

Introduction: To address United Nations Millennium Develop­ment Goal 4 (MDG 4) on reducing childhood mortality by three-quarter by 2015, there is a need for better population-based data on the rates and causes of neonatal death. This study aims to identify the risk factors of neonatal mortality in Bangladesh.Methods: The study used data from the nationally representative 2007 Bangladesh Demographic and Health Survey. The survey gathered information regarding socioeconomic, demographic, environmental and maternal and child health care of 10,996 ever married women and 6,058 children. Both bivariate and multivariate statistical analyses were used to assess the relationship between neonatal mortality and contextual factors.Results: The prevalence of neonatal mortality was 37/1,000. The statistical analyses yielded quantitatively important and reliable estimates of neonatal death. The multivariate logistic regression analysis yielded significantly increased risk of neonatal mortality for children with mother who had no formal education, the Muslims, whose mother were adolescents age 15-19, first ranked birth and twin babies.       Conclusion: Emphasis should be given to improve female education in Bangladesh for a better chance of satisfying important factors that can improve infant survival: the quality of infant feeding, general care, household sanitation, and adequate use of preventive and curative health services.Key words: Maternal and child health; Female education; MDG 4; Neonatal mortalityDOI: http://dx.doi.org/10.3126/jnps.v32i1.4845  J. Nepal Paediatr. Soc. Vol.32(1) 2012 37-46

Plant stature of aromatic rice genotypes in the environment of Bangladesh

Plant stature of a rice crop is an important selection criterion. As plant height is a quantitative trait it is influenced by environmental conditions. A field experiment was conducted with 40 rice genotypes to assess the fluctuation and stability of plant height in a series of 16 environmental situations. The effects of genotype (G), environment (E) and all the components of GxE interaction were highly significant. Among the genotypes, Jamai sohagi was extremely sensitive (bi = 1.37) to environmental changes, and indicating lowest adaptability over the environments. Plant height of seven genotypes viz. Basmati PNR346, Benaful, BRRIdhan28, BRRIdhan38, BRRIdhan39, Gandho kasturi and Neimat, having the bi values between 0.59 and 0.72, showed high stability against environmental changes. The otherseven genotypes viz. Badshabhog, Basmati Tapl-90, Kamini soru, Khazar, Laljira, Sarwati and Ukni madhu expressed only nonlinear sensitivity (S2di = 90-181)) and thus unpredictable fluctuation. Twenty one genotypes indicated their average stability (bi = 0.91-1.15) over the environments.

Antioxidant and antimicrobial attributes and phenolics of different solvent extracts from leaves, flowers and bark of Gold Mohar [Delonix regia (Bojer ex Hook.) Raf]

This paper describes the antioxidant and antimicrobial activities and phenolic components of different solvent (absolute methanol, absolute ethanol, absolute acetone, 80% methanol, 80% ethanol, 80% acetone and deionized water) extracts of leaves, flowers and bark of Gold Mohar [Delonix regia (Bojer ex Hook.) Raf.]. The extract yields from leaves, flowers and bark ranged from 10.19 to 36.24, 12.97 to 48.47 and 4.22 to 8.48 g/100 g dry weight (DW), respectively. Overall, 80% methanol extract produced from the leaves exhibited significantly (P < 0.05) higher antioxidant activity, with high phenolic contents (3.63 g GAE/100 g DW), total flavonoid contents (1.19 g CE/100 g DW), inhibition of peroxidation (85.54%), DPPH scavenging capacity (IC₅₀ value 8.89 μg/mL) and reducing power (1.87). Similarly, this 80% methanol leaves extract also showed superior antimicrobial activity. HPLC analysis of the 80% methanol extracts for individual phenolics revealed the presence of gallic, protocatechuic and salicylic acid in leaves; gallic, protocatechuic, salicylic, trans-cinnamic and chlorogenic acid in flowers, and gallic acid in bark as the main (amount > 1.50 mg/100 g DW) phenolic acids. Besides, small amounts (<1.50 mg/100 g DW) of some other phenolic acids such as sorbic, sinapic, p-coumaric, m-coumaric, ferulic, caffeic, 3-hydroxybenzoic, 4-hydroxycinnamic and 4-hydroxybenzoic acids were also detected. The extracts of the tested parts of Gold Mohar, especially, the leaves, might be valuable for functional food and therapeutic applications.

Entropic fragment-based approach to aptamer design

Aptamers are short RNA/DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA/DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.

Partial purification and characterization of polyphenol oxidase from banana (Musa sapientum L.) peel

Polyphenol oxidase (EC 1.10.3.1, o-diphenol: oxygen oxidoreductase, PPO) of banana (Musa sapientum L.) peel was partially purified about 460-fold with a recovery of 2.2% using dopamine as substrate. The enzyme showed a single peak on Toyopearl HW55-S chromatography. However, two bands were detected by staining with Coomassie brilliant blue on PAGE: one was very clear, and the other was faint. Molecular weight for purified PPO was estimated to be about 41 000 by gel filtration. The enzyme quickly oxidized dopamine, and its Km value (Michaelis constant) for dopamine was 3.9 mM. Optimum pH was 6.5 and the PPO activity was quite stable in the range of pH 5-11 for 48 h. The enzyme had an optimum temperature at 30 degrees C and was stable up to 60 degrees C after heat treatment for 30 min. The enzyme activity was strongly inhibited by sodium diethyldithiocarbamate, potassium cyanide, L-ascorbic acid, and cysteine at 1 mM. Under a low buffer capacity, the enzyme was also strongly inhibited by citric acid and acetic acid at 10 mM.

Purification and characterization of polyphenol oxidase from banana (Musa sapientum L.) pulp

Polyphenol oxidase (EC 1.10.3.1, PPO) in the pulp of banana (Musa sapientum L.) was purified to 636-fold with a recovery of 3.0%, using dopamine as substrate. The purified enzyme exhibited a clear single band on polyacrylamide gel electrophoresis (PAGE) and sodium dodecyl sulfate (SDS)-PAGE. The molecular weight of the enzyme was estimated to be about 41000 and 42000 by gel filtration and SDS-PAGE, respectively. The enzyme quickly oxidized dopamine, and its K(m) value for dopamine was 2.8 mM. The optimum pH was at 6.5, and the enzyme activity was stable in the range of pH 5-11 at 5 degrees C for 48 h. The enzyme had an optimum temperature of 30 degrees C and was stable even after a heat treatment at 70 degrees C for 30 min. The enzyme activity was completely inhibited by L-ascorbic acid, cysteine, sodium diethyldithiocarbamate, and potassium cyanide. Under a low buffer capacity, the enzyme was also strongly inhibited by citric acid and acetic acid at 10 mM.