Miracle-dz/UniFAR-FTUs huggingface dataset:
Aggregate formation in axenic and microbial co-inoculated batch cultures of aulacoseira granulata (bacillariophyceae)

Aggregate formation in axenic and microbial co-inoculated batch cultures of Aulacoseira granulata (Bacillariophyceae). Aggregate formation involving diatoms is a well-known process, especia l ly in the mar ine envi ronment . The a im of th is paper was to observe natura l aggregates formation in axenic and microbial coinoculated cultures of the freshwater diatom Aulacoseira granulata. The growth of bacteria and A. granulata were also monitored, as were qualitative alterations in the composition of the extracellular polysaccharide (EPS) produced by A. granulata in both axenic and microbial co-inoculated cultures. Aggregates were naturally formed in both conditions and our results suggested that the aggregation process increased significantly in the presence of a microbial community from Barra Bonita Reservoir. A. granulata biomass formation also signif icantly increased along bacterial growth and the EPS composition found in the microbial co-inoculated cultures was different to that of the axenic cultures. Rhamnose proportion increased around 50 % in microbial coinoculated cul tures, probably due to bacter ia l act iv i ty , increasing the hydrophobic properties of the EPS. The aggregation increase in the microbial co-inoculated cultures was correlated to the enhancement of the EPS hydrophobic nature, as wel l as to the biomass increase of A. granulata. Key-words: Aulacoseira granulata, aggregates, extracellular polysaccharide, microbial degradation, bacterial growth. RESUMO: Formação de agregados em culturas de Aulacoseira granulata (Bacillariophyceae) axênicas e inoculadas com bactérias. A formação de agregados envolvendo diatomáceas é já um processo bem conhecido, especialmente em ambientes marinhos. O objetivo deste trabalho foi observar a formação espontânea de agregados em culturas de Aulacoseira granulata axênicas e inoculadas com bactérias. O crescimento de bactérias e de A. granulata foi monitorado bem como as alterações qualitativas, causadas pela atividade bacteriana, na composição do polissacarídeo extracelular (EPS) l iberado pela diatomácea em ambas as culturas. A formação de agregados ocorreu em ambas as culturas, mas os resultados sugerem que a agregação aumenta significantemente na presença de bactérias de populações oriundas do reservatório de Barra Bonita, também o local de origem da diatomácea. A biomassa de A. granulata aumentou signif icantemente na presença de bactérias e a composição do EPS nas culturas contaminadas foi diferente daquele das culturas axênicas. A atividade bacteriana aumentou a porcentagem do monossacarídeo Ramnose em cerca de 50 % nas culturas contaminadas, aumentando as propriedades hidrofóbicas do EPS. Assumimos que o aumento da hidrofobicidade bem como o aumento da biomassa de A. granulata nas culturas contaminadas foram os fatores responsáveis pelo aumento da agregação dos filamentos de A. granulata nas culturas contaminadas. Palavras-chave: Aulacoseira granulata, agregados, polissacarídeo extracelular, degradação microbiana, crescimento bacteriano.
Development of a Bacteriophage Based Bioluminescent Bioreporter System for the Detection of Escherichia coli K12 and O157:H7

32 Introduction . 33 Materials and methods . 36 Bacterial strains and bacteriophage . 36 Genetic construction of the λluxI reporter bacteriophage . 37 Genetic construction of E. coli OHHLux . 40 Dose response kinetics of the E. coli OHHLux bioreporter to OHHL . 43 Specificity of the E. coli OHHLux bioreporter towards OHHL . 44 Phage reporter pure culture assay . 44 Lettuce leaf wash assays . 46 Analytical measurement of OHHL . 48 Results . 48 OHHL dose response of the E. coli OHHLux bioreporter. 48 Specificity of the E. coli OHHLux bioreporter towards OHHL . 50 Phage reporter assay in pure culture . 50 Lettuce leaf rinse assays. 53 vii Discussion . 55 Chapter III: Bacteriophage based bioluminescent bioreporter for the detection of E. coli O157:H7 . 61 Abstract . 62. 62 Introduction . 63 Materials and methods . 66 Bacterial strains and bacteriophage . 66 Construction of the reporter phage . 66 Detection of E. coli O157:H7 in pure culture . 73 Specificity of assay for E. coli O157:H7 . 74 Detection of E. coli O157:H7 in apple juice . 75 Results . 76 PP01-luxI reporter phage assay in pure culture . 76 Specificity of PP01-luxI reporter phage assay . 76 PP01-luxI reporter phage assay to detect E. coli O157:H7 in apple juice . 79 Discussion . 79 Part IV: Bacteriophage-amplified bioluminescent sensing of E. coli O157:H7 . 85 Abstract . 86. 86 Introduction . 87 viii Materials and methods . 89 Bacterial strains and bacteriophage . 89 96-well microtiter plate sampling formats for pure culture, apple juice, tap water, and ground beef detection assays . 90 Real-time bioluminescent imaging of E. coli O157:H7 in spinach leaf rinsate . 93 Results . 94 Determination of E. coli O157:H7 inoculum concentrations . 94 Detection of E. coli O157:H7 in pure culture . 95 Detection of E. coli O157:H7 in apple juice . 97 Detection of E. coli O157:H7 in tap water . 97 Detection of E. coli O157:H7 in ground beef . 100 CCD imaging of E. coli O157:H7 in spinach leaf rinsates . 100 Discussion . 101 Chapter V: Conclusions . 106 References . 110 Vita . 130
6 Morphology and Behavior: Are They Coupled at the Genome Level?

In all organisms, behavior and morphology are inextricably coupled. Morphology constrains the range of behavioral patterns, and behavior regulates and modifies morphological function. Over centuries, this constraint has been recognized in the selective breeding of dogs to perform specific tasks. Here, we explore the genetic coupling of morphology and behavior in a fox model system: the heritable morphological variation that has accompanied selection for tame and aggressive behavioral traits in the silver fox. In what follows, we demonstrate that similar functional trade-offs in morphology are found in both foxes and dogs and that this morphological variation may be concomitant with behavioral variation. Finally, we describe preliminary results from experiments designed to test whether these two phenotypes are related at the genetic level (thus co-selected) or have become associated serendipitously as a result of random genetic drift and founder effects. The red fox, Vulpes vulpes , of which the silver fox is a subspecies, is the out-group for modern canids. Its phylogenetic lineage has been separated from Canis familiaris for about 10 million years (Wayne 1993). V. vulpes has the largest natural geographic distribution of any terrestrial mammal other than humans. It occupies habitats ranging from mixed forest to alpine tundra, from sand dunes to urban outskirts (Nowak and Paradiso 1991; Sheldon 1992). Associated with this diversity of habitats is a wide range of anatomical configurations and a behavioral plasticity that makes the red fox the bane of chicken farmers, the favorite of hunting sportsmen, and a mythic symbol of crafty intelligence.
Fruit flies of economic significance in India, with special reference to Bactrocera dorsalis (Hendel).

India has nearly 200 species of fruit flies,which is about 5% of the known tephritid fauna of the world. The subfamily Dacinae has the maximum number of economically important species. The tribe Dacini with the genus Bactrocera is of importance in India. From an economic point of view, B. dorsalis (Hendel), B. correcta (Bezzi), B. zonata (Saunders) and B. cucurbitae (Coquillett) are important. The first three species mainly attack fruit crops, while B. cucurbitae attacks different species of cucurbits. In an Indian context, B. dorsalis is a major fruit fly pest, especially on mango, affecting local and export markets. The crop loss due to B. dorsalis varies with season and region. In Bangalore, it was found that the loss to mango in an unsprayed situation varied from 2.5 to 59.0% depending on the variety. The cultivars Dushehari and Langra were least infested, while cultivars Banganpalli and Totapuri had a mean infestation of 46.0 and 59.0%, respectively. In guava it is reported that B. dorsalis causes between 5 and 70% crop loss. An assortment of management strategies has been evaluated in India. A study from northeast India by Makhmoor & Singh (1997) showed that hoeing once a day, once in three days and once in seven days resulted in 80, 70 and 43% pupal mortality, respectively, of B. dorsalis. Soil type also influenced pupal mortality, with maximum mortality occuring on clayey soil. The use of the parapheromone ‘methyl eugenol’ in traps is quite popular in India. Of the different traps evaluated, namely IIHR bottle trap, Steiner trap, McPhail trap, delta trap, Jackson sticky trap and open pan trap, the IIHR bottle trap attracted the most flies. Trapping has been found to be useful both for monitoring and management. Using extracts of Ocimum sanctum in traps is also in vogue, but is less efficient than methyl eugenol. Pre-harvest sprays using either dimethoate 0.06%, carbaryl 0.2% or deltamethrin 0.0028% are also recommended. At the Indian Institute of Horticultural Research an IPM package for the management of B. dorsalis on mango is recommended, which consists of orchard sanitation together with inter-tree ploughing and raking plus three applications of insecticidal sprays of the above-mentioned chemicals on the fruits. This has given between 76 and 100% control. A double-walled steel tank of 1 cubic metre with a thermostat was manufactured to test post-harvest disinfestations of mango using hot water. It was found that a postharvest hot-water treatment at 48°C for 60 to 75 minutes gave satisfactory results. A combination of preand post-harvest management gave 100% control of B. dorsalis. The aim of this paper is to highlight the research findings on B. dorsalis in India, based on work carried out at IIHR, Bangalore, and elsewhere in the country. The distribution, species complex and other wild hosts of the genus Bactrocera are discussed.
Reassortant Avian Influenza A(H9N2) Viruses in Chickens in Retail Poultry Shops, Pakistan, 2009–2010

Phylogenetic analysis of influenza viruses collected during December 2009–February 2010 from chickens in live poultry retail shops in Lahore, Pakistan, showed influenza A(H9N2) lineage polymerase and nonstructural genes generate through inter- and intrasubtypic reassortments. Many amino acid signatures observed were characteristic of human isolates; hence, their circulation could enhance inter- or intrasubtypic reassortment.
An unexpected cerebral sinovenous thrombosis in a boy with acute lymphoblastic leukemia: A case report

Acute Lymphoblastic Leukemia (ALL) is the most common malignancy in children. Prednisone, Vincristine, Cytarabine and also L-Asparaginase are usually used in induction chemotherapy. Thrombovascular events such as Cerebral Sinovenous Thrombosis (CSVT) are one of the most common complications of the disease that may arise during or even after the treatment. Majority of the cases of CSVT are either directly attributed to ALL or considered as a consequence of using chemotherapy agents mentioned above. In this manuscript we present an 8-years-old boy diagnosed with ALL who exhibited seizure attack following his first chemotherapy cession. CSVT was finally diagnosed due to manifestations and assessments.
Leaf rust resistance in selections from barley landraces collected in Sardinia

Leaf rust caused by fungus Puccinia hordei has economic importance in many barley growing regions. Breeders are constantly looking for new effective sources of resistance to this pathogen. Landraces were proven to be rich source of resistance genes for resistance to major pathogens of barley. A total of 240 lines selected from 12 populations of barley landraces collected in Sardinia were tested for leaf rust resistance. Eight differential isolates of P. hordei were used. Plants of only 8 lines (4974, 4997, 5041, 5055, 5086, 5102, 5121 and 5132) originating from 5 populations of barley landraces (Sard 2, Sard 5, Sard 7, Sard 8, Sard 9) showed resistance to leaf rust. From total 8 lines showing resistance to leaf rust in 7 lines (4974, 4997, 5055, 5086, 5102, 5121 and 5132) were observed both plants resistant and susceptible after inoculation with isolate of leaf rust. Next after selection of resistant plants single plant lines were created (4974-4, 4997-1, 5041-3, 5055-1, 5086-3, 5102-1, 5121-1 and 5132-1) and resistance tests were performed with differential isolates of leaf rust. Only one line (4974-4) was resistant to infection with all isolates used. Identified leaf rust resistant lines, especially line 4974-4 should be used as source of leaf rust resistance in barley breeding programmes. Different strategies for control of barley leaf rust were discussed.
Factors affecting experimental Streptococcus agalactiae infection in tilapia, Oreochromis niloticus

Streptococcus agalactiae infection is one of the major disease problems affecting farmed tilapia (Oreochromis niloticus) worldwide. Tilapia are highly susceptible to this disease which results in mortality of up to 70% over a period of around 7 days and significant economic losses for farmers. Affected tilapia commonly present with an irregular behaviour associated with meningoencephalitis and septicaemia. Currently, factors affecting the virulence and transmission of S. agalactiae in fish including tilapia are poorly understood. Reports from natural outbreaks of S. agalactiae infection on tilapia farms have suggested larvae and juvenile or fish smaller than 20 g are not susceptible. In addition, there is variability in individual response to experimental inflammatory challenge associated with coping styles (bold, shy) in common carp (Cyprinus carpio). The central hypotheses of this thesis were that weight, age and coping style might affect the development and progression of this bacterial disease. This study investigated these three factors with experimental S. agalactiae infection in Nile tilapia. A range of bacterial isolates recovered from farmed tilapia, presenting with clinical sign of streptococcosis during natural disease outbreaks were identified and characterised as S. agalactiae by standard conventional methods, biochemical characteristic tests, Lancefield serogrouping and species-specific PCR assay. These isolates were Gram-positive cocci, either β- or non-haemolytic (γ), non-motile, oxidase negative and all of serogroup B. In addition, they were able to grow on Edwards medium (modified) agar as blue colonies and growth was observed in broth from 22 to 37 oC and with 0.5-5% NaCl. The biochemical profiles showed some differences in reactions while all the PCR samples showed similarities to the S. agalactiae type strain. These data confirmed that these strains were identified as group B S. agalactiae. A challenge model for S. agalactiae in Nile tilapia was developed and the LD50 estimated prior to performing subsequent experimental challenge studies. Two exposure routes, immersion and intraperitoneal injection (i.p.), were tested with various concentrations of S. agalactiae. Only i.p. injection produced significant mortalities (9 × 108 CFU/ml = 48% mortality, 9 × 107 = 48% and 8 × 106 = 26%). Streptococcus agalactiae was recovered and identified from all the dead and moribund fish during these experiments, where affected fish showed similar clinical signs and pathology to those reported from natural S. agalactiae infections. The study results showed that an experimental i.p. challenge model for S. agalactiae infection had successfully infected healthy Nile tilapia. In the immersion challenges, only 1 fish died despite testing a range of bacterial concentrations, exposure times, stocking density, water system and bacterial preparations. The experimental studies were conducted to investigate the association between weight or age of fish and susceptibility to S. agalactiae infection in Nile…
Biological control of taro scarab beetle (Papuanauninodis Coleoptera: Scarabaeidae) instars via Scoliid and Voria Tachinidae parasitoid wasps

Scoliid and Voria Tachinidae parasitoid wasps are shown to be able to control the population of the Taro Scarab beetle (Papuanauninodis, Coleoptera: Scarabaeidae) larvae using a newly created continuous-time simulation model based on non-linear ordinary differential equations that track the populations of the beetle’s life cycle stages: egg, larva, pupa, adult and the populations of the two parasitoid wasps. Due to the fact that the scarab beetles are, relatively speaking, long lived it is challenging to drive down the adult population below the environmental carrying capacity. Mortality and predator/prey capture rates are modelled using the Weibull and Pascal probability distribution functions, respectively. We suggest the use of a virus or fungi to drive down the population of the adult beetles, the ambition being to avoid the use of pesticides so as to produce higher quality food that doesn’t damage human health via chemical residues.
The Effects of Physiochemical Parameters on Planktonic Species Population of Keenjhar Lake, District Thatta, Sindh, Pakistan

The significance of Keenjhar Lake is due to irrigation, wild life sanctuary and supply of drinking water to the local population at vicinity. The objective of present studies was organized to explore the primary productivity and physicochemical properties of Keenjhar Lake. In present study 210 planktonic species were identified they belongs to 11 classes and 85 genera. Out of them 173 species were phytoplanktonic, 83 Cyanophyceae, 57 Chlorophyceae, 24 Bacillariophyceae, 5 Euglenophyceae, 2 species of Dinophyceae and 1 specie belonged to each Xanthophyceae and Chrysophyceae respectively. Whilst, a part of them 37 species were belonged to zooplankton comprising 15 species each of Cladocera and Rotifera, 4 species of Ostracoda and 3 species of Copepoda. The physicochemical properties such as (temperature, alkalinity, dissolved oxygen, electrical conductivity, total dissolved solids, and pH) were recorded from keenjhar lake district, Thatta, Sindh, Pakistan, range between 33.1-18.5°C, 223-170 mg L-1, 9.6-6.9 mg L-1, 512-350 µS cm-1, 410-270 mg L-1, and 8.9-7.6 respectively on monthly basis. The physicochemical properties of Keenjhar Lake were suitable for growth of aquatic biota.
Mass spectrometry of the subcutaneous interstitial fluid obtained by microdialysis in situ in lean man: A novel in vivo application of proteomics

Background: Obesity and the metabolic syndrome is a global problem, and it is known that the adipose tissue plays a crucial role in its development. Many methods exist to study this problem, but there is a need of a minimally invisive in vivo technique. The combination of microdialysis with Mass spectrometry could present a further insight into what mechanisms in the adipose tissue that promote development of the metabolic syndrome. Aim: To develop and evaluate a method for studies of the adipose tissue secretome in vivo. Method: Basic protocols for microdialysis and Mass spectrometry were adapted to one another before subcutaneous dialysates of 8 healthy subjects were run through the protocol. The proteins detected in all subjects were checked through a database for information regarding origin, function, size and if they were secreted or not. A general overview of the results was also made investigating the relation to protein concentration in the dialysate and the number of different proteins detected for each additional subject. Results: 531 proteins were detected, of which 63 were found in all subjects. Out of these 63 proteins, 87% were identified as secreted proteins, about half of them having an inflammatory or cell damage response function whereas the other proteins were transporters, metabolic proteins or had other functions. About 50% of the proteins were described as plasma proteins, a third had an unknown origin and all the remaining but one protein had an origin from a cell type within the adipose tissue. The correlation between the protein concentration in the collected dialysate and the amount of detected proteins was low. For each subject added to the study additional proteins unique for that sample were detected. There was a low variation between subjects regarding protein concentration of individual proteins. Conclusions: The method provides a unique insight to the adipose tissue secretome which previously did not exist. However, there is a large amount of cell damage and inflammation which to some extent may be caused by the inserted catheters. Therefore, when applying this method to a comparative study between two groups, inflammatory components will have to be interpreted with caution. Nevertheless, there are indications that the protocol could be further refined by simple means.
The Burden Experience of Formal and Informal Caregivers of Older Adults With Hip Fracture in Nigeria

Introduction The incidence of hip fracture among older adults in Nigeria is on the rise. As a result, there is increased frequency of hospitalization, patient suffering, family burden, and societal cost. One dimension that has not been sufficiently explored is the burden of care experienced by informal and formal caregivers. Objectives To describe the care burden experience of informal and formal caregivers for older adults with hip fractures in a specialized orthopedic center in Nigeria and to explore in detail how their experience differs in caregiving roles. Method This study was conducted in the phenomenological approach of qualitative methods. Face-to-face interviews and focus group interaction with 12 family caregivers and 5 health-care professionals were carried out until data saturation was achieved. Data were analyzed using thematic analysis. Results The physical, emotional, and general health of elderly hip fracture patients are issues that affect caregiving. Factors that contribute to increased caregivers’ burden include system factors (lack of personnel and health-care facilities) and patient factors: comorbidity, patient’s cognitive status, and challenges completing activities of daily living (ADL). Social and financial barriers to care contribute to the type of burden experienced by the participants. Conclusions Caregivers experience difficulty in helping patients complete their ADL because patients with hip fracture have mobility issues that are often complicated by comorbid physical and cognitive problems. Strategies to reduce caregivers’ burden for older adults with hip fracture in Nigeria are needed. Greater access to health-care services and ADL aids, and training of caregivers on how to deal with cognitive and multimorbid health problems are potential solutions.
Molecular analysis of persistent enterovirus infections.

1 1 INTRODUCTION . 2 2 – THE ENTEROVIRUS GENUS . 4 2.1 – ENTEROVIRUS STRUCTURE . 6 2.2 – ENTEROVIRUS GENOME . 8 2.2.1 – The RNA dependent RNA polymerase . 9 2.3 – ENTEROVIRUS RECEPTORS AND CELL ENTRY . 9 2.5 – ENTEROVIRUS LIFE CYCLE . 12 2.6 – CLINICAL DISEASES . 14 2.7 – FIGURES . 17 3 – PERSISTENT ENTEROVIRUS INFECTIONS . 21 3.1 – TYPE 1 DIABETES . 22 3.1. 1 – Enteroviruses and T1D . 24 3.1. 2 – Possible mechanisms of HEV pathogenesis in T1D . 25 3.3 – POST POLIO SYNDROME (PPS) . 28 3.3.1 – Viral persistence in PPS patients . 29 3.2 – VIRAL CARDIOMYOPATHY. 31 3.2.1 – Hypothesized viral cardiomyopathy mechanism . 32 3.4 – FIGURES . 35 4 ENTEROVIRUS DIAGNOSIS . 37 4.1 BIOLOGICAL APPROACH . 37 4.1. 1 Determination of neutralizing antibodies . 38 4.1. 2 ELISA for enterovirus antibodies . 40 4.1. 3 Immunofluorescence for enterovirus antibodies . 41 4.2 MOLECULAR APPROACH . 43 4.2.1 5’ UTR Methods . 43 4.2.2 Capsid amplification methods . 44 4.3 – FIGURES . 46 5 METHODS . 47 5.1 – SAMPLE PREPARATION . 47 5.2 CELL CULTURE AND REFERENCE HEV TYPES . 47 5.3 INDIRECT IMMUNOFLUORESCENCE (IIF) FOR CAPSID ANTIGEN DETECTION . 48