Miracle-dz/UniFAR-FTUs huggingface dataset:
Impacts of mucins on microbial physiology and interactions

The human body is colonized by trillions of microbes known collectively as the microbiota. Many of these organisms inhabit mucosal surfaces, with most found in the large intestines, but many also dwell in the respiratory and urogenital tracts. Despite the enormous microbial population inhabiting the body, some of which are opportunistic pathogens, most people harbor these organisms without showing any signs of disease. The mucus that covers the wet epithelium and houses the microbiota is a prime candidate for offering protection from pathogens, yet its specific role is poorly understood. The object of this thesis is to explore the effects of mucins, the main gel-forming component of mucus, on microbial behavior. Using an in vitro mucus model consisting of purified mucins, I show that these polymers suppress microbial virulence traits in selected bacterial and fungal opportunistic pathogens and influence the composition of microbial communities. In Chapter 2, I study the impact of mucins on bacterial biofilm formation using the opportunistic pathogen Pseudomonas aeruginosa. I demonstrate that mucins reduce surface attached biofilm formation. However, P. aeruginosa can overcome mucin-induced biofilm suppression if flagellar motility is lost, allowing them to form non-surface attached biofilms that are suspended in mucins. In Chapter 3, I analyze the effects of mucins on the virulence traits of Candida albicans, a fungal opportunistic pathogen. The results show that mucins broadly suppress virulence traits of this organism, such as surface attachment, hyphal formation and biofilm formation, at both the levels of gene expression and phenotype. In Appendix A, I combine P. aeruginosa and C. albicans with mucins to determine the influence of these molecules on interspecies interactions. Whereas P. aeruginosa typically kills C. albicans, mucins protect the fungus from bacterial pathogenicity. Therefore, in addition to influencing microbial virulence, mucins can impact microbial community dynamics. Overall, my work suggests that mucins protect the body from microbes by functioning as a modulator of microbial behavior, coercing certain microbes to downregulate virulence gene and trait expression, thereby influencing microbial effects on the host and within the microbiota. Thesis Supervisor: Katharina Ribbeck Title: Assistant Professor of Biological Engineering
Living Ostracod Species From Permanent and Semi-Permanent Ponds of Bardenas Reales De Navarra (Northern Spain) With Remarks on Their Ecological Requirements

Abstract. Ostracod species living in 13 ponds (25 sample points) in Bardenas Reales de Navarra Natural Park and World Biosphere Reserve are studied for the first time. Nineteen species were identified, nine of them being the most abundant. According to statistical analyses (cluster and Correspondence Analysis), the distribution of ostracod species in this semi-arid area is mainly controlled by water conductivity and pH. The hydroperiod, sediment type, dissolved oxygen, altitude and vegetation cover play a secondary role. Thus, in semi-permanent waters with conductivity between 4.5 and 5.4 mS/cm and pH from 7.95 to 8.73 the most abundant species is Sarscypridopsis aculeata (Costa). In ponds with water conductivity from 0.3 to 2 mS/cm, pH between 7.1 and 7.78 and dissolved oxygen from 0.1 to 7.95 mg/l, Cypridopsis vidua (Müller) s the most abundant species. When the vegetation cover increases in this type of ponds, Limnocythere inopinata (Baird) and Potamocypris villosa (Jurine) appear as more abundant. Finally, in ponds with conductivity between 0.34 and 2.8 mS/cm and sporadic input of running waters llyocypris bradyi Sars, is the most important species. When the internal water current increases in these ponds, Pseudocandona albicans (Brady) appears as most abundant. However, the accumulation of dead organic matter within the bottom sediment of these ponds favours the decrease of dissolved oxygen and the development of Eucypris virens (Jurine). With this work, we contribute to the knowledge of the ostracod biodiversity of this semi-arid environment and the ecological preferences of this group.
Evidence for some signal transduction elements involved in UV-light-dependent responses in parsley protoplasts

The signalling pathways used by UV-light are largely unknown. Using protoplasts from a heterotrophic parsley (Petroselinum crispum L.) cell culture that exclusively respond to UV-B light between 300 and 350 nm with a fast induction of genes encoding flavonoid biosynthetic enzymes, information was obtained about the UV-light signal transduction pathway for chalcone synthase (CHS) and phenylalanine ammonia-lyase (PAL) gene expression. Pharmacological effectors which influence intracellular calcium levels, calmodulin and the activity of serine/ threonine kinases also changed the UV-light-dependent expression of these genes. This evaluation indicated the participation of these components on the UV-B-mediated signal transduction cascade to CHS. In contrast, neither membrane-permeable cyclic GMP nor the tyrosine kinase inhibitor genistein affected CHS or PAL expression. Similar results were obtained in protoplasts, which have been transiently transformed with CHS-promoter/GUS β-glucuronidase) reporter fusion constructs. The involvement of calcium and calmodulin was further indicated in a cell-free light-responsive in vitro transcription system from evacuolated parsley protoplasts. In conclusion, there is evidence now that components of the UV-light-dependent pathway leading to the CHS-promoter are different from the previously characterized cGMP-dependent pathway to CHS utilized by phytochrome in soybean (Glycine max) and tomato seedlings (Lycopersicon esculentum).
Standardization of Polyphenol Content for certain Species Belonging to Genus Pelargonium cultivated in Egypt

Traditionally, Pelargonium species due to its tannin contents; was used to staunch bleeding, heal wounds, ulcers, uterine hemorrhage, a comparative study was carried out on Pelargonium peltatum L’Herit and Pelargonium x fragrans In order to incorporate these two active extracts into pharmaceutical preparations, they need to be standardized by quantitative means. The total polyphenol contents of the aqueous extract of both plants were determined by Folin-Ciocalteu assay for estimation the total polyphenol (TP) contents of the aqueous extract. TP were expressed as mg of gallic acid equivalents (GAE)/g of the dry plant material, revealed that it was relatively high in both species representing 12.46 and 12.67 mg GAE/g dry weight respectively.
Preliminary Results to the Holistic Knowledge of the Amphipoda Hyperiidea Faunal Composition off the Brazilian Coast

Little information is available on hyperiidean amphipods from the tropical and subtropical areas of the south-western Atlantic Ocean. Forty-nine samples were collected during the FINEP XI Cruise (23-27°S/41-48°W). from Cabo Frio to Santa Catarina Island in January 1980. Zooplankton was collected with a 333 μm mesh size net on the continental shelf. The material comprised mainly specimens from the Infraorder Physocephalata, members of which usually inhabit the surface and middle depths of the ocean. Forty species belonging to 27 genera and 14 families were identified, resulting in 12 new records for the Brazilian coast. Laxohyperia vespuliformis Vinogradov and Volkov, 1982 and Amphithyrus muratus Volkov, 1982 are recorded from the Atlantic Ocean for the first time. Twelve instances of association were observed between hyperiids and gelatinous zooplankton (salps and siphonophores). Qualitative and quantitative variations in the species composition are analysed in accordance with the bathymetric and hydrological local conditions. The present study is a step towards a better understanding of the taxonomy and distribution of the Amphipoda Hyperiidea in Brazillian waters.
Effect of falciparum malaria on some plasma proteins in males: With special reference to the levels of testosterone and cortisol

Sex-associated hormones were evidenced to modulate immune responses and consequently directly influence the outcome of infection. Testosterone is known to influence both protein metabolism and the level of cortisol which is the hormone of stress. This work was conducted to explore the influence of the degree of parasitemia in Plasmodium falciparum malaria on the male sex hormone testosterone, plasma proteins and the stress hormone cortisol in male patients. The study targeted male subjects whose ages ranged between 20 and 40 years old. The subjects were divided into three groups: lightlyinfected patients (Infected with P. falciparum density 1 - 10 asexual form of the parasite per 100 fields), heavily-infected patients (Infected with P. falciparum density 11 - 99 asexual form of the parasite per 100 fields) and a group of malaria-free individuals who were used as a control group. Blood samples were taken from the median cephalic vein to investigate for malaria parasite, plasma proteins and hormones. The effect of the degree of parasitemia was considered for all parameters studied. The study revealed that low parasitemia in malaria-infected patients resulted in significantly (p < 0.05) higher level of plasma total proteins and it was found to be due to a significant (P < 0.05) increase in the total globulins fraction which reached 5.85 ± 1.03 g/dl compared to 3.44 ± 0.4 g/dl in the control group. The opposite was true for the heavily-infected group as it reported significantly (P < 0.05) lower total plasma proteins value which was found to be due to a significant (p < 0.05) reduction of the total globulins fraction reported only 2.96 ± 0.20 g/dl. The albumin fraction maintained levels similar to that of the control group in both infected groups. The levels of the hormones tested also showed significant changes, manifested as significantly (p < 0.05) lower values in both groups of patients compared to the control group for the testosterone hormone, with significant (p < 0.05) difference between the two groups. Thus, high parasitemia resulted in the least testosterone level in the heavily-infected group of 2.64 ± 0.28 ng/ml, compared to 6.03 ± 0.86 ng/ml in the control group. In contrast, the stress hormone, the cortisol, showed the highest level in the heavily-infected patients of 191.03 ± 18.17 ng/ml, with significant (p < 0.05) difference compared to 166.28 ± 10.63 ng/ml in the control group.
Cloning and Expression of a Rat Brain Interleukin-1β-Converting Enzyme (ICE)-Related Protease (IRP) and Its Possible Role in Apoptosis of Cultured Cerebellar Granule Neurons

Several members of the IL-1β-converting enzyme (ICE) family of proteases recently have been implicated in the intracellular cascade mediating the apoptotic death of various cell types. It is unclear, however, whether ICE-related proteases are involved in apoptosis of mammalian neurons and, if so, how they are activated. Here we report the cloning of an ICE-related protease (IRP) from rat brain, which displays strong sequence identity to human CPP32. In situ hybridization histochemistry reveals that this IRP mRNA is expressed in neuron-enriched regions of the developing and adult rat brain but is profoundly downregulated in the adult (compared with developing) brain. To investigate whether this IRP is involved in the death of neurons in the developing brain, we studied IRP expression in cultured cerebellar granule neurons. In cultured cerebellar granule neurons, reduction of extracellular K+ reliably induces apoptosis and stimulates overexpression of IRP mRNA. The latter is especially prominent 4 hr after switching from high K+ to low K+ medium. The expression of IRP mRNA was maintained at this level for at least 8 hr and was followed by apoptotic death of these neurons. Induction of IRP mRNA and cell death are blocked completely by adding depolarizing concentrations of K+ ≤90 min after switching to low K+ medium (i.e., before the commitment point for apoptosis) and partially blocked by brain-derived neurotrophic factor (BDNF), which also partially rescues granule neurons from low K+-induced apoptosis. In addition, overexpression of IRP cDNA in HeLa cells results in cell death accompanied by strong internucleosomal cleavage of DNA, a typical feature of apoptosis. Finally, we detected cleavage of the putative death substrate poly (ADP-ribose) polymerase (PARP), beginning 8 hr after changing from high K+ to low K+ medium, coinciding with the time course of induced expression of the IRP gene. Our data suggest that transcriptional activation of IRP could be one of the mechanisms involved in the apoptotic death of cerebellar granule neurons.
Isolation and characterization of rhamnolipid producing Pseudomonas aeruginosa strains from waste edible oils

This study was to screen efficient biosurfactant producing strains from waste edible oils (WEOs). Two strains Y5 and Y17 were screened out by steps of preliminary blood plate screening and secondary flask fermentation screening. The surface tension of the fermentation broth of the two strains diluted by 100 times was lower than 40 mN/m. Preliminary characterization of fermentation products was conducted, which was found to be rhamnolipid ultimately. Y5 strain produced only one kind of glycolipids while the Y17 produced at least three kinds of homologues of glycolipids. Both Y5 and Y17 were identified as Pseudomonas aeruginosa strains. This study gave a simple and efficient protocol to screen out biosurfactant producing strains and would pave the way for the production of biosurfactant from WEOs. Key words: Rhamnolipid, biosurfactant, fermentation, waste edible oils, Pseudomonas aeruginosa.
Stomatal conductance and photosynthesis

This research is part of an effort that the ICT (Institute of Tropical Cultivation) has been doing for several years tending to develop superior genotypes of cocoa (Theobroma cacao L.). That is why this study aims to find tolerant or moderately tolerant cocoa genotypes and accessions to water stress with resistance to pests and diseases and high production and industrial quality. Twenty genotypes of cocoa seedlings were investigated, during the period of 6 months, in a soil with sandy-loam texture under nursery conditions, of controlled irrigation. A split plot design was used, with 40 treatments and 3 repetitions. In addition, daily data of the micro climatic characteristics (T °, HR) were taken, in which different indicators of variable were evaluated such as the stomatal conductance (CE) that is greatly influenced by the T ° and HR. The results obtained indicate that the genotypes that showed moderate tolerance to water stress were UNG - 77, UNG - 53, ICT - 1281 and ICT - 1112; the non-tolerant ones were PAS - 93, CEPEC - 2002, ICT - 2142, ICT - 1092, CP - 2005 - C10, TSH - 1188, CCN - 51, IMC - 67, PH - 17, AYP - 15, ICS - 6, BN - 34, ICT - 1506, PAS - 91, PH - 990 and ICS - 1. Under optimal conditions, the most outstanding genotype was ICS-1, both in plant height, number of leaves, and stomatal conductance, this being proof that this genotype develops excellently and stands out if it has the right conditions and water availability.
Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton

We investigated to what extent chitinolytic bacteria subsidize bacterial populations that do not produce chitinolytic enzymes but still use the products of chitin hydrolysis. Applying single‐cell techniques to untreated and chitin‐enriched lake water, we show that the number of planktonic cells taking up chitin hydrolysis products by far exceeds the number of cells expressing chitinases. Flavobacteria, Actinobacteria, and specifically members of the abundant and ubiquitous freshwater Ac1 cluster of the Actinobacteria, increased in abundance and were enriched in response to the chitin amendment. Flavobacteria were frequently observed in dense clusters on chitin particles, suggesting that they are actively involved in the hydrolysis and solubilization of chitin. In contrast, Actinobacteria were exclusively planktonic. We propose that planktonic Actinobacteria contain commensals specialized in the uptake of small hydrolysis products without expressing or possibly even possessing the machinery for chitin hydrolysis. More research is needed to assess the importance of such “cheater” substrate acquisition strategies in the turnover and degradation of polymeric organic matter in aquatic ecosystems.
A monoclonal antibody that recognizes a carbohydrate epitope on N -linked glycoproteins restricted to a subset of chitin-rich fungi

Previous studies with a monoclonal antibody (designated UB7) raised against isolated haustorial complexes formed by the pea powdery mildew fungus Erysiphe pisi showed that it recognized an abundant glycoprotein found in cell walls and plasma membranes of haustoria and the surface mycelium. In this paper, Western blotting and phase-partitioning in the detergent Triton X-114 have been used to show that the plasma membrane antigens recognized by UB7 comprise a 62 kDa integral glycoprotein and a set of integral membrane glycoproteins of lower molecular weight. A 59 kDa glycoprotein recognized by UB7 has been extracted from the fungus using aqueous buffer, and the evidence suggests that this represents the cell wall form of the antigen. Binding of UB7 is abolished by pre-treatment of glycoproteins with peptide-N-glycosidase, but is retained after endo-F treatment. This suggests that the epitope to which UB7 binds is the innermost N-acetylglucosamine residue of N-linked carbohydrate side chains of glycoproteins, possibly substituted with one or more sugars. When tested for cross-reactivity with other fungi, UB7 bound to some, but not all, of those examined, and recognized different sets of glycoproteins compared with those detected in E. pisi. However, UB7 did not bind to any higher plants nor to any animal glycoproteins tested. This antibody thus identifies a carbohydrate epitope restricted to glycoproteins in a subset of the fungi.
Over‐wintering stage polymorphism of a bruchine beetle: geographical variation in optimal diapause strategy

Abstract 1. Most temperate insects undergo diapause at a specific developmental stage to overcome severe winters. The bruchine beetle Bruchidius dorsalis in a warmer region in Japan, however, has diverse over‐wintering stages – non‐diapausing larvae, diapausing larvae, and diapausing adults, whereas in a cooler region, it over‐winters only as the final instar larva or adult in diapause.
Isolasi dan Karakterisasi Amilase dari Biji Durian (Durio sp.)

ABSTRAK Amilase merupakan enzim yang mampu menghidrolisis ikatan glikosidik dalam molekul pati. Amilase berasal dari berbagai sumber yaitu, mikroorganisme, tumbuhan, dan manusia. Penggunaan biji durian sebagai sumber amilase merupakan bentuk pemanfaatan limbah. Biji durian dipilih sebagai sumber amilase karena mengandung amilum. Karbohidrat yang terdapat pada biji durian memungkinkan adanya amilase. Tujuan umum dari penelitian ini adalah untuk mengisolasi dan mengkarakterisasi amilase dari biji durian. Amilase diekstraksi dengan buffer fosfat 50 mM (pH 7,5). Amilase difraksinasi dengan metode salting out menggunakan (NH4)2SO4 dan dimurnikan dengan metode didialisis. Aktivitas amilase dari biji durian (Durio sp.) ditentukan dengan menggunakan metode Fuwa dan konsentrasi protein diukur dengan metode Bradford. Aktivitas spesifik yang paling tinggi diperoleh pada tingkat kejenuhan 60% sebesar 1959,75 U/mg. pH optimum amilase berada pada pH 6 sedangkan suhu optimumnya berada pada suhu 40 oC.
Nutritive value of wheat concentrated distillers solubles in diets for growing pigs

Two experiments (Exp.) were conducted to determine the nutritive value of wheat-derived wet concentrated distillers solubles (CDS) for growing pigs. In Exp. 1, standardised ileal digestibility (SID) of amino acids (AA) was determined by the difference method, using six ileally cannulated barrows (initial bodyweight (BW) of 31 ± 2.9 kg). The pigs were fed a casein-corn starch-based diet supplemented with wheat CDS so that about half of the crude protein (CP) originated from either wheat CDS or from casein. In Exp. 2, 12 barrows with an initial BW of 17 ± 0.9 kg were used to determine digestible energy (DE) content, and to calculate metabolisable energy (ME) and net energy (NE) content of wheat CDS. Animals were fed either a casein-corn starch-based basal diet or a CDS diet containing 470 g/kg of the basal diet and 530 g/kg wheat CDS on a dry matter (DM) basis. Values of SID of CP and AA in Exp. 1 amounted to 85, 74, 83 and 70% for CP, lysine, methionine and threonine, respectively. The DE, ME and NE contents of wheat CDS were 16.8, 15.8 and 11.1 MJ/kg DM, respectively. It can be concluded that SID of CP and AA and also the energy content in wheat CDS are substantially higher than corresponding values reported in international tables with information on nutritional value of dried co-products of bioethanol production.
Vibrio tapetis sp. nov., the Causative Agent of the Brown Ring Disease Affecting Cultured Clams

A taxonomic characterization was carried out on strains of the bacteria that cause the brown ring disease of clams. On the basis of their phenotypic and genotypic characteristics, these strains can be considered to constitute a new taxonomic unit, distinct from other Vibrio species. The guanine-plus-cytosine content of the strains ranged between 42.9 and 45.5 mol% (43.2 mol% for the proposed type strain). DNA-DNA hybridization studies showed 100% intragroup relatedness, but levels of genetic relatedness to the reference strains of different Vibrio species tested ranged between 15 and 58%. The strains have all the properties characteristic of the genus Vibrio and can be clearly differentiated from other species of this genus by their growth at 4°C and their negative responses for growth at 30°C and in 6% NaCl, arginine dehydrolase, lysine decarboxylase, ornithine decarboxylase, and Voges-Proskauer reaction. The name Vibrio tapetis is proposed for the new species; strain B1090 (CECT 4600) is the type strain.
Freshwater availability and coastal wetland foundation species: ecological transitions along a rainfall gradient

Climate gradient-focused ecological research can provide a foundation for better understanding critical ecological transition points and nonlinear climate–ecological relationships, which is information that can be used to better understand, predict, and manage ecological responses to climate change. In this study, we examined the influence of freshwater availability upon the coverage of foundation plant species in coastal wetlands along a northwestern Gulf of Mexico rainfall gradient. Our research addresses the following three questions: (1) What are the regional-scale relationships between measures of freshwater availability (e.g., rainfall, aridity, freshwater inflow, salinity) and the relative abundance of foundation plant species in tidal wetlands; (2) how vulnerable are foundation plant species in tidal wetlands to future changes in freshwater availability; and (3) what is the potential future relative abundance of tidal wetland foundation plant species under alternative climate change scenarios? We .