Identification, Genome Sequencing, and Characterizations of Helicobacter pylori Sourced from Pakistan.

The stomach's colonization by Helicobacter pylori (H. pylori) results in gastritis, ulcers, and stomach cancer. Frequently, pain is treated with medication, but resistant H. pylori infections are not. Therefore, it is important to find pharmacological targets and improved treatments for resistant H. pylori strains. The aim of the current study was sampling, identification, drug susceptibility testing following genome sequencing and comparative genome-wide analysis of selected H. pylori strains from Pakistan with three representative strains for virulence and drug-resistant characteristics. Based on culture, biochemistry, and molecular biology, 84 strains of H. pylori were identified, which made up 47% of the enrolled cases. Among all H. pylori strains, the highest resistance was reported for metronidazole with 82 H. pylori strains (98%), followed by clarithromycin with 62 resistant strains (74%). Among metronidazole-resistant strains, 38 strains (46%) were also resistant to clarithromycin, contributing 61% of clarithromycin resistant cases. Two strains, HPA1 and HPA2, isolated from 'gastritis' and 'gastric ulcer' patients, respectively, were further processed for WGS. The draft genome sequences of H. pylori strains HPA1 and HPA2 encode 1.66 Mbp and 1.67 Mbp genome size, 24 and 4 contiguous DNA sequences, and 1650 and 1625 coding sequences, respectively. Both the genomes showed greater than 90% similarity with the reference strain H. pylori ATCC 43504/PMSS1. The antibiotic-resistant genes were identified among all the strains with overall similarity above 95%, with minor differences in the sequence similarity. Using the virulent gene data obtained from the Virulence Factor Database, 75 to 85 virulent genes were identified in the five genome assemblies with various key genes such as cytolethal distending toxin (cdt), type IV secretion system, cag PAI, plasticity region, cell-motility- and flagellar-associated genes, neutrophil-activating protein (HP-NAP), T4SS effector cytotoxin-associated gene A (cagA), and urease-associated genes ureA and ureB, etc. Sequence similarity between the virulence factors found in this study and reference genes was at least 90%. In summary, the results of our study showed the relationship between clinical results and specific H. pylori strains' (HPA1 and HPA2) genetics such as antibiotic resistance and specific virulence factors. These findings provide valued understanding of the epidemiology of H. pylori-associated diseases. Moreover, identification and genomics analysis have provided insights into the epidemiology, genetic diversity, pathogenicity, and potential drug resistance genes of H. pylori strains, offering a foundation for developing more targeted and effective medical interventions, including anti-virulent medications.

Novel microalgae strains from selected lower Himalayan aquatic habitats as potential sources of green products.

Microalgal biomass provides a renewable source of biofuels and other green products. However, in order to realize economically viable microalgal biorefinery, strategic identification and utilization of suitable microalgal feedstock is fundamental. Here, a multi-step suboptimal screening strategy was used to target promising microalgae strains from selected freshwaters of the study area. The resulting strains were found to be affiliated to seven closely-related genera of the family Scenedesmaceae, as revealed by both morphologic and molecular characterization. Following initial screening under upper psychrophilic to optimum mesophilic (irregular temperature of 14.1 to 35.9°C) cultivation conditions, superior strains were chosen for further studies. Further cultivation of the selected strains under moderate to extreme mesophilic cultivation conditions (irregular temperature of 25.7 to 42.2°C), yielded up to 74.12 mgL-1day-1, 19.96 mgL-1day-1, 48.56%, 3.34 µg/mL and 1.20 µg/mL, for biomass productivity, lipid productivity, carbohydrate content, pigments content and carotenoids content respectively. These performances were deemed promising compared with some previous, optimum conditions-based reports. Interestingly, the fatty acids profile and the high carotenoids content of the studied strains revealed possible tolerance to the stress caused by the changing suboptimal cultivation conditions. Overall, strains AY1, CM6, LY2 and KL10 were exceptional and may present sustainable, promising feedstock for utilization in large-scale generation of green products, including biodiesel, bioethanol, pigments and dietary supplements. The findings of this study, which exposed promising, eurythermal strains, would expand the current knowledge on the search for promising microalgae strains capable of performing under the largely uncontrolled large-scale cultivation settings.

The Effectiveness of Protected Areas in Conserving Globally Threatened Western Tragopan Tragopan melanocephalus.

Protected areas are a critical tool to conserve biodiversity in the face of the global crisis of species extinction. Here, we present the first ever management effectiveness assessment of Pakistan's Protected Areas (PAs). We link these assessments to the delivery of conservation outcomes focusing on the threatened Western Tragopan (Tragopan melanocephalus) endemic to Pakistan and India. We used two approaches, first mapping the spatial distribution of potential habitat coverage using machine learning ensemble models and second, an assessment of the management effectiveness of protected areas. Our results show that only Machiara National Park scored just above 40% (indicating relatively weak management), 22 of the PAs fell within the 25-50% quantile (indicating weak management), and 3 scored below 25% (indicating poor management). PAs within the species distributional range covered 92,387 ha which is only 2% of the total potential habitat of the Tragopan. Scoring of Planning element was insufficient both in term of the site and species. Likewise, inputs (e.g., research and monitoring program, staff numbers, staff training, current budget, security of budget, and management after process) were also inadequate. Finally, we recommend the establishment of more protected areas within the species potential habitat and inclusion of species-specific plans in Pakistan's PAs management.

Photocatalytic Decolorization and Biocidal Applications of Nonmetal Doped TiO2: Isotherm, Kinetic Modeling and In Silico Molecular Docking Studies.

Textile dyes and microbial contamination of surface water bodies have been recognized as emerging quality concerns around the globe. The simultaneous resolve of such impurities can pave the route for an amicable technological solution. This study reports the photocatalytic performance and the biocidal potential of nitrogen-doped TiO2 against reactive black 5 (RB5), a double azo dye and E. coli. Molecular docking was performed to identify and quantify the interactions of the TiO2 with ß-lactamase enzyme and to predict the biocidal mechanism. The sol-gel technique was employed for the synthesis of different mol% nitrogen-doped TiO2. The synthesized photocatalysts were characterized using thermal gravimetric analysis (TGA), scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Brunauer-Emmett-Teller (BET) and diffuse reflectance spectroscopy (DRS). The effects of different synthesis and reaction parameters were studied. RB5 dye degradation was monitored by tracking shifts in the absorption spectrum and percent chemical oxygen demand (COD) removal. The best nanomaterial depicted 5.57 nm crystallite size, 49.54 m2 g-1 specific surface area, 11-40 nm particle size with spherical morphologies, and uniform distribution. The RB5 decolorization data fits well with the pseudo-first-order kinetic model, and the maximum monolayer coverage capacity for the Langmuir adsorption model was found to be 40 mg g-1 with Kads of 0.113 mg-1. The LH model yielded a higher coefficient KC (1.15 mg L-1 h-1) compared to the adsorption constant KLH (0.3084 L mg-1). 90% COD removal was achieved in 60 min of irradiation, confirmed by the disappearance of spectral peaks. The best-optimized photocatalysts showed a noticeable biocidal potential against human pathogenic strain E. coli in 150 min. The biocidal mechanism of best-optimized photocatalyst was predicted by molecular docking simulation against E. coli ß-lactamase enzyme. The docking score (-7.6 kcal mol-1) and the binding interaction with the active site residues (Lys315, Thr316, and Glu272) of ß-lactamase further confirmed that inhibition of ß-lactamase could be a most probable mechanism of biocidal activity.

Corrigendum to "Combined Industrial Wastewater Treatment in Anaerobic Bioreactor Post-Treated in Constructed Wetland".

[This corrects the article DOI: 10.1155/2013/957853.].

Risk Assessment of Heavy Metals in Selected Marine Fish Species of Gadani Shipbreaking Area and Pakistan.

Gadani shipbreaking area, located on the coastline of Pakistan, is an important fish production area. In this study, levels of four metals (Ni, Pb, Cd, and Mn) in 148 muscle and gill samples of seven fish species (Small-scale terapon, Torpedo scade, Sicklefish, Saddle grunt, Gold silk seabream, Indian mackerel, Spotted sickle fish) and seawater samples, taken from 9 sampling sites in the shipbreaking area, were determined. In addition, multiple approaches were used to assess human health risks from fish consumption. Trace metal concentration in seawater ranged from 0.05 to 1.96 mg/L in shipbreaking vicinity and 0.03 to 0.97 mg/L in the reference site (Miani Hor). However, metal accumulations in fish species ranged from 1.33 to 5.26 µg/g. Among trace metals, the level of Pb in all fish species was highest, followed by Ni, Mn, and Cd. The bioaccumulation factors (BAFs) for both gills and muscles displayed the order: Mn > Cd > Ni > Pb. Estimated daily intake (EDI) values were below the tolerable daily intake (TDI). Based on target hazard quotient (THQ), the investigated fish species were safe regarding Pb and Mn (THQ < 1), while they may cause potential risk regarding Cd and Ni (THQ > 1). After comparison with maximum permissible limits, heavy metal concentration in the edible muscle tissues of all the analyzed fish species from the Gadani coast were found safe for human consumption.

Gene expression and biochemical response of giant reed under Ni and Cu stress.

Giant reed (Arundo donax) has proved to be effective in detoxification, accumulation and tolerance of toxic metals. The present study explored the stress response of giant reed against Cu and Ni stress. The effect of metal stress was studied on dry weight, chlorophyll pigments antioxidant enzymes production and selected genes expression. The accumulation of heavy metals increased in a concentration-dependent manner and depicted toxicity symptoms in leaves beyond 75 mg/L of Cu or Ni. Oxidative stress was evident in giant reed under highest exposure of Ni and Cu which increased antioxidants activities (SOD, POD and CAT). It was observed that metal transport and detoxification were possible due to the expression of glutathione reductase, Natural Resistance-Associated Macrophage Protein (NRAMP) and Yellow Stripe-Like (YSL) genes. These insights into the genetic basis of a successful remediating plant species will be useful in understanding heavy metals tolerance in giant reed.

Residues of endosulfan in cotton growing area of Vehari, Pakistan: an assessment of knowledge and awareness of pesticide use and health risks.

This study is based on self-reported information collected from selected farmers of Vehari District, Punjab, Pakistan, to determine their technical knowledge and awareness about pesticide use and associated environmental and health risks. Moreover, soil contamination by routinely used persistent organochlorine pesticide, endosulfan, was also evaluated. Survey data revealed very low literacy rate (on an average 9th grade education) and technical knowledge (almost missing) of the farmers in Vehari District. The farmers are unable to fully read and understand the instructions about the use of pesticide marked on the containers. They are not fully aware of pesticide persistence and toxicity (73%), unable to identify cotton pests and diseases (86%), and do not know which crop to grow in cotton adjacent fields (100%). Data also revealed that the farmers (100%) do not follow safety measure during pesticide application and are unaware of pesticide toxicity symptoms in human as well as the basic first-aid practices (89%).Poor literacy rate and lack of technical knowledge of farmers in Vehari regarding pesticide use and handling are posing serious environmental and health risks among the local inhabitants, particularly among farmers. Soil analysis results showed that concentration of α- and ß-endosulfan ranged from 0-14 to 0-14.64 µg/mg, respectively. Principal component analysis showed that soil organic matter is the key soil parameter controlling the occurrence and fate of endosulfan under sandy loam soil conditions of Vehari District. There is a serious need of improving technical and environmental knowledge of farmer about pesticide risks on human health in the studied area, in particular, and the entire country in general. Findings are of great use for policymaking in Pakistan to minimize pesticide risks in Pakistan.

A newly isolated Pseudomonas sp. can degrade endosulfan via hydrolytic pathway.

Endosulfan an organochlorinated pesticide was used extensively throughout the world. Its enormous and inadequate use creates environmental as well as health problems. A bacterial strain capable to utilize endosulfan as a sole source of sulfur was isolated from pesticide contaminated soil and identified as Pseudomonas sp. on the basis of 16S rRNA. Batch experiments were conducted at various initial concentrations of endosulfan, i.e. 5, 25, 50, 75 and 100 mg/l to study its rate of degradation. After three days of incubation, 70-80% of each initial concentration was degraded by the isolated strain as compared to the control. Degradation of endosulfan increased with the time of incubation and maximum degradation was observed after 5 days of incubation. GC-MS revealed that the major metabolite was endosulfan lactone, which accumulated after 5 days of incubation. Kinetic studies at various initial concentrations also revealed that the bacterium has very promising attitude to utilize endosulfan as sole source of sulfur. It was observed that the addition of auxiliary sulfur Fe(SO4)3 in any concentration (0.05, 0.01 and 0.1%) decreased the rate of degradation of endosulfan. The ratio of µmax/ Ks was high (0.03 mg/l) when endosulfan was single sulfur source as compared to the value recorded when Fe(SO4)3 was added alongwith the endosulfan. This indicates that the newly isolated bacterium attacks sulfur moiety for its degradation.

Corrigendum to "Plants as Useful Vectors to Reduce Environmental Toxic Arsenic Content".

[This corrects the article DOI: 10.1155/2014/921581.].

Corrigendum to "Natural Treatment Systems as Sustainable Ecotechnologies for the Developing Countries".

[This corrects the article DOI: 10.1155/2013/796373.].

Improvement in lipids extraction processes for biodiesel production from wet microalgal pellets grown on diammonium phosphate and sodium bicarbonate combinations.

Biomass productivity and growth kinetics for microalgae grown on sodium bicarbonate and diammonium phosphate were investigated. Different carbon and nitrogen ratios have shown different growth rates and biomass productivity and C:N ratio 50:10 as mgL(-1) has shown the best production than all. For effective lipids extraction from biomass thermolysis and sonolysis were carried out from wet biomass. Sonolysis at 2.3W intensity for 5min has released 8.58mg at neutral pH. More quantity of lipids was extracted when extraction was made at pH 4 and 10 which resulted 9mg and 9.28mg lipids respectively. Thermal treatment at 100°C for 10min has released 12.82mg lipid at neutral pH. In the same thermolysis at pH 4 and 10 more quantity of lipids was extracted which were 15.16mg and 14.81mg respectively. Finally transesterified lipids were analyzed through GC-MS for FAME composition analysis.

Biochemical and Metabolic Changes in Arsenic Contaminated Boehmeria nivea L.

Arsenic (As) is identified by the EPA as the third highest toxic inorganic contaminant. Almost every 9th or 10th human in more than 70 countries including mainland China is affected by As. Arsenic along with other toxins not only affects human life but also creates alarming situations such as the deterioration of farm lands and desertion of industrial/mining lands. Researchers and administrators have agreed to opt for phytoremediation of As over costly cleanups. Boehmeria nivea L. can soak up various heavy metals, such as Sb, Cd, Pb, and Zn. But the effect of As pollution on the biology and metabolism of B. nivea has been somewhat overlooked. This study attempts to evaluate the extent of As resistance, chlorophyll content, and metabolic changes in As-polluted (5, 10, 15, and 20 mg L(-1) As) B. nivea in hydroponics. Toxic effects of As in the form of inhibited growth were apparent at the highest level of added As. The significant changes in the chlorophyll, electrolyte leakage, and H2O2, significant increases in As in plant parts, catalase (CAT), and malondialdehyde (MDA), with applied As revealed the potential of B. nivea for As decontamination. By employing the metabolic machinery of B. nivea, As was sustainably removed from the contaminated areas.

Anaerobic microbial fuel cell treating combined industrial wastewater: Correlation of electricity generation with pollutants.

Microbial fuel cell (MFC) is a new technology that not only generates energy but treats wastewater as well. A dual chamber MFC was operated under laboratory conditions. Wastewater samples from vegetable oil industries, metal works, glass and marble industries, chemical industries and combined industrial effluents were collected and each was treated for 98h in MFC. The treatment efficiency for COD in MFC was in range of 85-90% at hydraulic retention time (HRT) of 96h and had significant impact on wastewater treatment as well. The maximum voltage of 890mV was generated when vegetable oil industries discharge was treated with columbic efficiency of 5184.7C. The minimum voltage was produced by Glass House wastewater which was 520mV. There was positive significant co-relation between COD concentration and generated voltage. Further research should be focused on the organic contents of wastewater and various ionic species affecting voltage generation in MFC.

Phytoaccumulation of heavy metals in natural plants thriving on wastewater effluent at Hattar industrial estate, Pakistan.

The objective of this research was to compare the potential of native plants for the phytoaccumulation of heavy metals (HM). Thirteen predominant plant species (including trees, bushes and grasses) namely Ricinus communis, Ipomoea carnea, Cannabis sativa, Parthenium hysterophorus, Acacia nilotica, Dalbergia sissoo, Acacia modesta, Solanum nigrum, Xanthium stromarium, Chenopodium album, Cynodon dactylon, Eleusine indica, and Dactyloctenium aegyptium were collected from the wastewater originated from Hattar industrial estate of Pakistan, Plants shoots and roots were analyzed for heavy metals/metalloid: Pb, Cr, Cd, Zn, Fe, Ni, and As. Among plant species, the accumulation potential for HM varied depending on the type of element. Regardless of the plant species, HM concentrations varied in the order of Fe>Zn>Cr>Pb>Ni>Cd>As. Tree species of R. communis, A. nilotica, A. modesta, and D. sissoo exhibited an enhanced concentrations of metals. Accumulation pattern of Fe, Pb, Cd, and As in plants could be related to the HM composition of soil and wastewater. Most of the species exhibited higher HM composition in the root as compared to shoot. The species that found with greater ability to absorb HM in the root, got higher HM concentrations in its shoot. Shoot tissue concentrations of HM were attained by the species as D. sissoo>A. modesta>A. nilotica>R. communis>I. carnea>C. album>E. indica>P. hysterophorus>S. nigrum>C. sativa>D. aegyptium>X. strumarium>C. dactylon. Based on results, tree plants were noticed as higher accumulators of HM in polluted soils.

Microbial ecology of anaerobic digesters: the key players of anaerobiosis.

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

Plants as useful vectors to reduce environmental toxic arsenic content.

Arsenic (As) toxicity in soil and water is an increasing menace around the globe. Its concentration both in soil and environment is due to natural and anthropogenic activities. Rising arsenic concentrations in groundwater is alarming due to the health risks to plants, animals, and human beings. Anthropogenic As contamination of soil may result from mining, milling, and smelting of copper, lead, zinc sulfide ores, hide tanning waste, dyes, chemical weapons, electroplating, gas exhaust, application of municipal sludge on land, combustion of fossil fuels, As additives to livestock feed, coal fly ash, and use of arsenical pesticides in agricultural sector. Phytoremediation can be viewed as biological, solar-driven, pump-and-treat system with an extensive, self-extending uptake network (the root system) that enhances the natural ecosystems for subsequent productive use. The present review presents recent scientific developments regarding phytoremediation of arsenic contaminated environments and its possible detoxification mechanisms in plants.

Waste biomass adsorbents for copper removal from industrial wastewater--a review.

Copper (Cu(2+)) containing wastewaters are extensively released from different industries and its excessive entry into food chains results in serious health impairments, carcinogenicity and mutagenesis in various living systems. An array of technologies is in use to remediate Cu(2+) from wastewaters. Adsorption is the most attractive option due to the availability of cost effective, sustainable and eco-friendly bioadsorbents. The current review is dedicated to presenting state of the art knowledge on various bioadsorbents and physico-chemical conditions used to remediate Cu(2+) from waste streams. The advantages and constraints of various adsorbents were also discussed. The literature revealed the maximum Cu adsorption capacities of various bioadsorbents in the order of algae>agricultural and forest>fungal>bacterial>activated carbon>yeast. However, based on the average Cu adsorption capacity, the arrangement can be: activated carbon>algal>bacterial>agriculture and forest-derived>fungal>yeast biomass. The data of Cu removal using these bioadsorbents were found best fit both Freundlich and Langmuir models. Agriculture and forest derived bioadsorbents have greater potential for Cu removal because of higher uptake, cheaper nature, bulk availability and mono to multilayer adsorption behavior. Higher costs at the biomass transformation stage and decreasing efficiency with desorption cycles are the major constraints to implement this technology.

Natural treatment systems as sustainable ecotechnologies for the developing countries.

The purpose of natural treatment systems is the re-establishment of disturbed ecosystems and their sustainability for benefits to human and nature. The working of natural treatment systems on ecological principles and their sustainability in terms of low cost, low energy consumption, and low mechanical technology is highly desirable. The current review presents pros and cons of the natural treatment systems, their performance, and recent developments to use them in the treatment of various types of wastewaters. Fast population growth and economic pressure in some developing countries compel the implementation of principles of natural treatment to protect natural environment. The employment of these principles for waste treatment not only helps in environmental cleanup but also conserves biological communities. The systems particularly suit developing countries of the world. We reviewed information on constructed wetlands, vermicomposting, role of mangroves, land treatment systems, soil-aquifer treatment, and finally aquatic systems for waste treatment. Economic cost and energy requirements to operate various kinds of natural treatment systems were also reviewed.

Combined industrial wastewater treatment in anaerobic bioreactor posttreated in constructed wetland.

Constructed wetland (CW) with monoculture of Arundo donax L. was investigated for the posttreatment of anaerobic bioreactor (ABR) treating combined industrial wastewater. Different dilutions of combined industrial wastewater (20, 40, 60, and 80) and original wastewater were fed into the ABR and then posttreated by the laboratory scale CW. The respective removal efficiencies of COD, BOD, TSS, nitrates, and ammonia were 80%, 78-82%, 91.7%, 88-92%, and 100% for original industrial wastewater treated in ABR. ABR was efficient in the removal of Ni, Pb, and Cd with removal efficiencies in the order of Cd (2.7%) > Ni (79%) > Pb (85%). Posttreatment of the ABR treated effluent was carried out in lab scale CW containing A. donax L. CW was effective in the removal of COD and various heavy metals present in ABR effluents. The posttreatment in CW resulted in reducing the metal concentrations to 1.95 mg/L, 0 mg/L, and 0.004 mg/L for Ni, Pb, and Cd which were within the permissible water quality standards for industrial effluents. The treatment strategy was effective and sustainable for the treatment of combined industrial wastewater.