XSS-haavoittuvuudet ja niiden havaitseminen web-sovelluksissa

Internet ja web-sovellukset ovat olennainen osa nykymaailmaa ja jatkuvan suosion myötä niiden tietoturva on yhä tärkeämmässä asemassa. Cross-site Scripting (XSS) on yksi yleisimmistä web-sovellusten haavoittuvuuksista. XSS-haavoittuvuutta hyödyntävällä hyökkäyksellä voidaan muokata web-sivuston sisältöä mielivaltaisesti, kaapata käyttäjän selainistunto tai varastaa käyttäjätietoja. Tässä tutkielmassa käsitellään menetelmiä XSS-haavoittuvuuksien havaitsemiseen web-sovelluksissa. Jos haavoittuvuudet voidaan havaita ajoissa, ne voidaan korjata ennen kuin niitä hyväksikäytetään hyökkäyksissä. Tutkielmassa käsitellään ja vertaillaan XSS-haavoittuvuuksien havaitsemismenetelmiä. Tutkimus toteutetaan kirjallisuuskatsauksena. Menetelmät on jaettu niiden käyttämän analyysimenetelmän perusteella kolmeen kategoriaan, jotka ovat staattinen analyysi, dynaaminen analyysi ja hybridianalyysi. Käsitellyillä menetelmillä on mahdollista havaita XSS-haavoittuvuuksia web-sovelluksissa tarkasti ja kattavasti. Uusimmissa menetelmissä hyödynnetään syväoppimista, vahvistusoppimista ja geneettisiä algoritmeja. Menetelmien kyky havaita haavoittuvuuksia on parantunut jatkuvasti vuoden 2015 jälkeen. Menetelmät ovat edistyneitä, mutta ne ovat usein rajoittuneita toimimaan vain tiettyjen ympäristöjen tai ohjelmointikielten kanssa. Lisäksi monet menetelmistä kykenevät havaitsemaan vain yhdenlaisia XSS-haavoittuvuuksia. Näihin ongelmiin olisi hyvä pyrkiä löytämään ratkaisuja tulevaisuudessa

Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle

<p>Abstract</p> <p>Background</p> <p>The assortment of cattle immunoglobulin and surrogate light chain genes has been extracted from the version 3.1 of <it>Bos taurus </it>genome sequence as a part of an international effort to sequence and annotate the bovine genome.</p> <p>Results</p> <p>63 variable lambda chain and 22 variable kappa chain genes were identified and phylogenetically assigned to 8 and 4 subgroups, respectively. The specified phylogenetic relationships are compatible with the established ruminant light chain variable gene families or subgroups. Because of gaps and uncertainties in the assembled genome sequence, the number of genes might change in the future versions of the genome sequence. In addition, three bovine surrogate light chain genes were identified. The corresponding cDNAs were cloned and the expression of the surrogate light chain genes was demonstrated from fetal material.</p> <p>Conclusion</p> <p>The bovine kappa gene locus is compact and simple which may reflect the preferential use of the lambda chain in cattle. The relative orientation of variable and joining genes in both loci are consistent with a deletion mechanism in VJ joining. The orientation of some variable genes cannot be determined from the data available. The number of functional variable genes is moderate when compared to man or mouse. Thus, post-recombinatorial mechanisms might contribute to the generation of the bovine pre-immune antibody repertoire. The heavy chains probably contribute more to recombinational immunoglobulin repertoire diversity than the light chains but the heavy chain locus could not be annotated from the version 3.1 of <it>Bos taurus </it>genome.</p

Identification of major cell types in paraffin sections of bovine tissues

BACKGROUND: Identification of cell types in bovine tissue sections is complicated by the limited availability of anti-bovine antibodies, and by antigen retrieval treatments required for formalin-fixed tissue samples. We have evaluated an antibody and lectin panel for identifying major cell types in paraffin-embedded bovine tissue sections, and report optimized pretreatments for these markers. RESULTS: We selected 31 useful antibodies and lectins which can be used to identify cell types of epithelia, connective tissue, muscle, and nervous tissue, as well as cell proliferation and apoptosis. CONCLUSION: The panel of markers allows the identification of all major cell types in paraffin-embedded cattle tissue sections by immunohistochemistry or lectin histochemistry. Heat-induced epitope retrieval methods are required for most antibodies

Direct observation of hematopoietic progenitor chimerism in fetal freemartin cattle

<p>Abstract</p> <p>Background</p> <p>Cattle twins are well known as blood chimeras. However, chimerism in the actual hematopoietic progenitor compartment has not been directly investigated. Here, we analyzed fetal liver of chimeric freemartin cattle by combining a new anti-bovine CD34 antibody and Y-chromosome specific in situ hybridization.</p> <p>Results</p> <p>Bull-derived CD34⁺cells were detected in the liver of the female sibling (freemartin) at 60 days gestation. The level of bull-derived CD34⁺cells was lower in the freemartin than in its male siblings. Bull (Y⁺) and cow hematopoietic cells often occurred in separate clusters. Around clusters of Y⁺CD34⁺cells, Y⁺CD34^-cells were typically observed. The thymi were also strongly chimeric at 60 days of gestation.</p> <p>Conclusion</p> <p>The fetal freemartin liver contains clusters of bull-derived hematopoietic progenitors, suggesting clonal expansion and differentiation. Even the roots of the hematopoietic system in cattle twins are thus strongly chimeric from the early stages of fetal development. However, the hematopoietic seeding of fetal liver apparently started already before the onset of functional vascular anastomosis.</p

Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta

Background The maternal microbiota affects the development of the offspring by microbial metabolites translocating to the fetus. To reveal the spectrum of these molecular mediators of the earliest host-microbe interactions, we compared placenta, fetal intestine and brain from germ-free (GF) and specific pathogen free (SPF) mouse dams by non-targeted metabolic profiling. Results One hundred one annotated metabolites and altogether 3680 molecular features were present in significantly different amounts in the placenta and/or fetal organs of GF and SPF mice. More than half of these were more abundant in the SPF organs, suggesting their microbial origin or a metabolic response of the host to the presence of microbes. The clearest separation was observed in the placenta, but most of the molecular features showed significantly different levels also in the fetal intestine and/or brain. Metabolites that were detected in lower amounts in the GF fetal organs included 5-aminovaleric acid betaine, trimethylamine N-oxide, catechol-O-sulphate, hippuric and pipecolic acid. Derivatives of the amino acid tryptophan, such as kynurenine, 3-indolepropionic acid and hydroxyindoleacetic acid, were also less abundant in the absence of microbiota. Ninety-nine molecular features were detected only in the SPF mice. We also observed several molecular features which were more abundant in the GF mice, possibly representing precursors of microbial metabolites or indicators of a metabolic response to the absence of microbiota. Conclusions The maternal microbiota has a profound impact on the fetal metabolome. Our observations suggest the existence of a multitude of yet unidentified microbially modified metabolites which pass through the placenta into the fetus and potentially influence fetal development.Peer reviewe

The composition of the perinatal intestinal microbiota in cattle

Publisher correction: Scientific reports 8, article number 13792 (2018) WOS:000444279700001Recent research suggests that the microbial colonization of the mammalian intestine may begin before birth, but the observations are controversial due to challenges in the reliable sampling and analysis of low-abundance microbiota. We studied the perinatal microbiota of calves by sampling them immediately at birth and during the first postnatal week. The large size of the bovine newborns allows sampling directly from rectum using contamination-shielded swabs. Our 16S rDNA data, purged of potential contaminant sequences shared with negative controls, indicates the existence of a diverse low-abundance microbiota in the newborn rectal meconium and mucosa. The newborn rectal microbiota was composed of Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The microbial profile resembled dam oral rather than fecal or vaginal vestibular microbiota, but included typical intestinal taxa. During the first postnatal day, the rectum was invaded by Escherichia/Shigella and Clostridia, and the diversity collapsed. By 7 days, diversity was again increasing. In terms of relative abundance, Proteobacteria were replaced by Firmicutes, Bacteroidetes and Actinobacteria, including Faecalibacterium, Bacteroides, Lactobacillus, Butyricicoccus and Bifidobacterium. Our observations suggest that mammals are seeded before birth with a diverse microbiota, but the microbiota changes rapidly in the early postnatal life.Peer reviewe

Faecal microbiota in two-week-old female dairy calves during acute cryptosporidiosis outbreak-Association with systemic inflammatory response

In the present study, relationships between the intestinal microbiota and innate immunity response, acute cryptosporidiosis, and weight gain in female dairy calves were investigated. A total of 112 calves born during a natural outbreak of cryptosporidiosis on one dairy farm was included in the study. Microbiota composition was analysed by means of 16S ribosomal RNA gene amplicon sequencing from faecal samples collected during the second week of life, while the status of Cryptosporidium spp. infection was determined using immunofluorescence. Serum samples from the second week of life were colourimetrically analysed for the following markers of acute inflammation: acute-phase proteins (serum amyloid A and haptoglobin) and pro-inflammatory cytokines (interleukin-1 beta, interleukin-6, and tumour necrosis factor-alpha). Statistical analyses were performed using random forest analysis, variance-partitioning, and negative binomial regression. The faecal microbiota of the two-week old calves was composed of the phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria (in order of decreasing abundance). Microbial diversity, measured in terms of the Shannon index, increased with the age of the calves and decreased if a high count of Cryptosporidium spp. oocysts was found in the faeces. Fusobacterium was positively associated with Cryptosporidium spp. oocyst count and serum amyloid A concentration. Peptostreptococcus was positively associated with haptoglobin and serum amyloid A concentrations, and negatively associated with average daily weight gain at 9 months of age. The markers of innate immunity, in combination with age, explained 6% of the microbial variation. These results suggest that some components of the intestinal microbiota may have a long-lasting negative effect on animal growth through the stimulation of the systemic innate immune response.Peer reviewe

Western diet enhances intestinal tumorigenesis in Min/ plus mice, associating with mucosal metabolic and inflammatory stress and loss of Apc heterozygosity

Western-type diet (WD) is a risk factor for colorectal cancer, but the underlying mechanisms are poorly understood. We investigated the interaction of WD and heterozygous mutation in the Apc gene on adenoma formation and metabolic and immunological changes in the histologically normal intestinal mucosa of Apc(Min/+) (Min/ +) mice. The diet used was high in saturated fat and low in calcium, vitamin D, fiber and folate. The number of adenomas was twofold higher in the WD mice compared to controls, but adenoma size, proliferation or apoptosis did not differ. The ratio of the MM to wild-type allele was higher in the WD mice, indicating accelerated loss of Apc heterozygosity (LOH). Densities of intraepithelial CD3 epsilon(+) T lymphocytes and of mucosal FoxP3(+) regulatory T cells were higher in the WD mice, implying inflammatory changes. Western blot analyses from the mucosa of the WD mice showed suppressed activation of the ERK and AKT pathways and a tendency for reduced activation of the mTOR pathway as measured in phosphoS6/S6 levels. The expression of pyruvate dehydrogenase kinase 4 was up-regulated in both mRNA and protein levels. Gene expression analyses showed changes in oxidation/reduction, fatty acid and monosaccharide metabolic pathways, tissue organization, cell fate and regulation of apoptosis. Together, our results suggest that the high-risk Western diet primes the intestine to tumorigenesis through synergistic effects in energy metabolism, inflammation and oxidative stress, which culminate in the acceleration of LOH of the Apc gene. (C) 2016 Elsevier Inc. All rights reserved.Peer reviewe

The Composition of the Microbiota in the Full-Term Fetal Gut and Amniotic Fluid : A Bovine Cesarean Section Study

The development of a healthy intestinal immune system requires early microbial exposure. However, it remains unclear whether microbial exposure already begins at the prenatal stage. Analysis of such low microbial biomass environments are challenging due to contamination issues. The aims of the current study were to assess the bacterial load and characterize the bacterial composition of the amniotic fluid and meconium of full-term calves, leading to a better knowledge of prenatal bacterial seeding of the fetal intestine. Amniotic fluid and rectal meconium samples were collected during and immediately after elective cesarean section, performed in 25 Belgian Blue cow-calf couples. The samples were analyzed by qPCR, bacterial culture using GAM agar and 16S rRNA gene amplicon sequencing. To minimize the effects of contaminants, we included multiple technical controls and stringently filtered the 16S rRNA gene sequencing data to exclude putative contaminant sequences. The meconium samples contained a significantly higher amount of bacterial DNA than the negative controls and 5 of 24 samples contained culturable bacteria. In the amniotic fluid, the amount of bacterial DNA was not significantly different from the negative controls and all samples were culture negative. Bacterial sequences were identified in both sample types and were primarily of phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with some individual variation. We conclude that most calves encounter in utero maternal-fetal transmission of bacterial DNA, but the amount of bacterial DNA is low and viable bacteria are rare.Peer reviewe

Modeling the role of highly oxidized multifunctional organic molecules for the growth of new particles over the boreal forest region

In this study, the processes behind observed new particle formation (NPF) events and subsequent organicdominated particle growth at the Pallas AtmosphereEcosystem Supersite in Northern Finland are explored with the one-dimensional column trajectory model ADCHEM. The modeled sub-micron particle mass is up to similar to 75% composed of SOA formed from highly oxidized multifunctional organic molecules (HOMs) with low or extremely low volatility. In the model the newly formed particles with an initial diameter of 1.5 nm reach a diameter of 7 nm about 2 h earlier than what is typically observed at the station. This is an indication that the model tends to overestimate the initial particle growth. In contrast, the modeled particle growth to CCN size ranges (> 50 nm in diameter) seems to be underestimated because the increase in the concentration of particles above 50 nm in diameter typically occurs several hours later compared to the observations. Due to the high fraction of HOMs in the modeled particles, the oxygen-to-carbon (O V C) atomic ratio of the SOA is nearly 1. This unusually high O V C and the discrepancy between the modeled and observed particle growth might be explained by the fact that the model does not consider any particle-phase reactions involving semi-volatile organic compounds with relatively low O V C. In the model simulations where condensation of low-volatility and extremely low-volatility HOMs explain most of the SOA formation, the phase state of the SOA (assumed either liquid or amorphous solid) has an insignificant impact on the evolution of the particle number size distributions. However, the modeled particle growth rates are sensitive to the method used to estimate the vapor pressures of the HOMs. Future studies should evaluate how heterogeneous reactions involving semi-volatility HOMs and other less-oxidized organic compounds can influence the SOA composition-and size-dependent particle growth.Peer reviewe