Browsing by Subject "diagnostics"

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  • Alakuijala, Anniina; Sarkanen, Tomi; Jokela, Tomi; Partinen, Markku (2021)
    Actigraphy provides longitudinal sleep data over multiple nights. It is a less expensive and less cumbersome method for measuring sleep than polysomnography. Studies assessing accuracy of actigraphy compared to ambulatory polysomnography in different sleep-disordered patients are rare. We aimed to compare the concordance between these methods in clinical setting. We included 290 clinical measurements of 281 sleep laboratory patients (mean age 37.9 years, 182 female). Concomitant ambulatory polysomnography and actigraphy were analyzed to determine the agreement in patients with obstructive sleep apnea, narcolepsy, periodic leg movement disorder, hypersomnia, other rarer sleep disorders, or no organic sleep disorder. Bland-Altman plots showed excellent accuracy, but poor precision in single night results between the two methods in the measurement of sleep time, sleep efficiency, and sleep latency. On average, actigraphy tended to overestimate sleep time by a negligible amount, -0.13 min, 95% confidence interval [-5.9, 5.6] min in the whole sample. Overestimation was largest, -12.8 [-25.1, -0.9] min, in patients with obstructive sleep apnea. By contrast, in patients with narcolepsy, actigraphy tended to underestimate sleep time by 24.3 [12.4, 36.1] min. As for sleep efficiency, actigraphy underestimated it by 0.18 [-0.99, 1.35] % and sleep latency by 11.0 [8.5, 13.6] min compared to polysomnography. We conclude that, in measuring sleep time, actigraphy is reasonably reliable and helpful to be used for a week or two to exclude insufficient sleep in patients with the suspicion of narcolepsy. However, the effectiveness of actigraphy in determining sleep seems to decrease in subjects with low sleep efficiencies.
  • Räisänen, Ismo T.; Lähteenmäki, Hanna; Gupta, Shipra; Grigoriadis, Andreas; Sahni, Vaibhav; Suojanen, Juho; Seppänen, Hanna; Tervahartiala, Taina; Sakellari, Dimitra; Sorsa, Timo (2021)
    The aim of this cross-sectional study is to propose an efficient strategy based on biomarkers adjunct with an interview/questionnaire covering risk factors for periodontitis for the identification of undiagnosed periodontitis by medical professionals. Active matrix metalloproteinase (aMMP)-8 levels in mouthrinse were analyzed by a point-of-care (PoC)/chairside lateral-flow immunotest, and salivary total MMP-8, total MMP-9 and calprotectin levels were analyzed by enzyme-linked immunosorbent assays (ELISAs) and active MMP-9 by gelatin zymography for 149 Greek patients. Patients underwent a full-mouth oral health examination for diagnosis according to the 2018 classification system of periodontal diseases. In addition, patient characteristics (risk factors: age, gender, education level, smoking and body mass index) were recorded. Receiver operating curve (ROC) analysis indicated better diagnostic precision to identify undiagnosed periodontitis for oral fluid biomarkers in adjunct with an interview/questionnaire compared with a plain questionnaire (i.e., risk factors): aMMP-8 AUC (95% confidence interval) = 0.834 (0.761-0.906), total MMP-8 = 0.800 (0.722-0.878), active MMP-9 = 0.787 (0.704-0.870), total MMP-9 = 0.773 (0.687-0.858) and calprotectin = 0.773 (0.687-0.858) vs. questionnaire = 0.764 (0.676-0.851). The findings of this study suggest that oral fluid biomarker analysis, such as a rapid aMMP-8 PoC immunotest, could be used as an adjunct to an interview/questionnaire to improve the precision of timely identification of asymptomatic, undiagnosed periodontitis patients by medical professionals. This strategy appears to be viable for referring patients to a dentist for diagnosis and treatment need assessment.
  • Chandola, Chetan; Kalme, Sheetal; Casteleijn, Marco G.; Urtti, Arto; Neerathilingam, Muniasamy (2016)
    Aptamers are small, single-stranded oligonucleotides (DNA or RNA) that bind to their target with high specificity and affinity. Although aptamers are analogous to antibodies for a wide range of target recognition and variety of applications, they have significant advantages over antibodies. Since aptamers have recently emerged as a class of biomolecules with an application in a wide array of fields, we need to summarize the latest developments herein. In this review we will discuss about the latest developments in using aptamers in diagnostics, drug delivery and imaging. We begin with diagnostics, discussing the application of aptamers for the detection of infective agents itself, antigens/toxins (bacteria), biomarkers (cancer), or a combination. The ease of conjugation and labelling of aptamers makes them a potential tool for diagnostics. Also, due to the reduced off-target effects of aptamers, their use as a potential drug delivery tool is emerging rapidly. Hence, we discuss their use in targeted delivery in conjugation with siRNAs, nanoparticles, liposomes, drugs and antibodies. Finally, we discuss about the conjugation strategies applicable for RNA and DNA aptamers for imaging. Their stability and self-assembly after heating makes them superior over protein-based binding molecules in terms of labelling and conjugation strategies.
  • Woock, Malin; Martinez-Majander, Nicolas; Seiffge, David J.; Selvik, Henriette Aurora; Nordanstig, Annika; Redfors, Petra; Lindgren, Erik; Sanchez van Kammen, Mayte; Rentzos, Alexandros; Coutinho, Jonathan M.; Doyle, Karen; Naess, Halvor; Putaala, Jukka; Jood, Katarina; Tatlisumak, Turgut (2022)
    The association between stroke and cancer is well-established. Because of an aging population and longer survival rates, the frequency of synchronous stroke and cancer will become even more common. Different pathophysiologic mechanisms have been proposed how cancer or cancer treatment directly or via coagulation disturbances can mediate stroke. Increased serum levels of D-dimer, fibrin degradation products, and CRP are more often seen in stroke with concomitant cancer, and the clot retrieved during thrombectomy has a more fibrin- and platelet-rich constitution compared with that of atherosclerotic etiology. Multiple infarctions are more common in patients with active cancer compared with those without a cancer diagnosis. New MRI techniques may help in detecting typical patterns seen in the presence of a concomitant cancer. In ischemic stroke patients, a newly published cancer probability score can help clinicians in their decision-making when to suspect an underlying malignancy in a stroke patient and to start cancer-screening studies. Treating stroke patients with synchronous cancer can be a delicate matter. Limited evidence suggests that administration of intravenous thrombolysis appears safe in non-axial intracranial and non-metastatic cancer patients. Endovascular thrombectomy is probably rather safe in these patients, but probably futile in most patients placed on palliative care due to their advanced disease. In this topical review, we discuss the epidemiology, pathophysiology, and prognosis of ischemic and hemorrhagic strokes as well as cerebral venous thrombosis and concomitant cancer. We further summarize the current evidence on acute management and secondary preventive therapy.
  • Snellman, Marja (2007)
    Community-acquired pneumonia (CAP) is a severe disease and a major cause of death worldwide especially among the elderly. The most common causative pathogen is Streptococcus pneumoniae, pneumococcus. The diagnosis of pneumococcal pneumonia is difficult because there is no gold standard, a diagnostic test that would identify all cases and yet be definite. National Public Health Institute has launched a Finnish Community-Acquired Pneumonia study investigating the frequency and causes of CAP among the elderly aged 65 years and above. Sputum, urine, blood and nasopharyngeal swab samples are the collected from the subjects enrolled in the study and a large number of microbiological assays are performed on samples. One of the main objectives is to find a case definition for pneumococcal pneumonia in the elderly. For this purpose, the accuracy of diagnostic tests performed in the study need to be evaluated. In the absence of gold standard, the true disease status of the subjects is latent and the sensitivities and the specificities of the tests cannot be estimated using conventional methods. The aim of this thesis is to to estimate the sensitivities and the specificities of diagnostic tests and estimate the prevalence of pneumococcal pneumonia among the elderly population in Finland using latent class analysis. The method is applied to data collected in the Finnish Community-Acquired Pneumonia study. Methodological issues in latent class analysis are discussed. In addition, a function for estimating the model parameters using statistical program R is presented. The main sources are: Agresti, Alan 2002: Categorical Data Analysis. Wiley. New York. Hagenaars, Jacques A. 1990: Categorical Longitudinal Data. Sage Publication. London Formann, A. - Kohlmann, T. 1996: Latent class analysis in medical research. Statistical Methods in Medical Research, 5, 179-211.
  • Viljamaa-Dirks, Satu (Evira, 2008)
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    Crayfish utilization is a long-standing Scandinavian tradition, which unfortunately has suffered a major drawback with the introduction of crayfish plague disease about a hundred years ago. In spite of intensive research many problems in management and diagnosis of this disease are not yet solved. To evaluate ongoing research and diagnostic methodology in different countries, representatives of diagnostic laboratories involved in crayfish disease diagnostics were invited to a workshop in Kuopio to discuss the problems with crayfish diseases. The workshop was held at the Kuopio unit of the Finnish Food Safety Authority Evira. Participants from Finland, Sweden, Norway, Estonia and Latvia were present, as well as the OIE expert from the reference laboratory for crayfish plague. In the programme of the first day the state of crayfish stocks, crayfish diseases and diagnostic methods used in each country were presented and discussed. During the second day diagnostic methods were discussed in detail, as well as research projects concerning crayfish diseases. The workshop has been made possible by way of a grant from the Nordic Council of Ministers.
  • Virtanen, Jenni; Aaltonen, Kirsi; Vapalahti, Olli; Sironen, Tarja (2020)
    Aleutian disease (AD), caused by Aleutian mink disease virus (AMDV), causes significant welfare problems to mink, and financial losses to the farmers. As there is no vaccine or treatment available, reliable diagnostics is important for disease control. Here, we set up a probe-based real-time PCR (NS1-probe-PCR) to detect all strains of AMDV. PCR was validated and compared to two other real-time PCR methods (pan-AMDV- and pan-AMDO-PCR) currently used for AMDV diagnostics in Finland. The NS1-probe-PCR had a similar detection limit of 20 copies/reaction based on plasmid dilution series, and similar or better diagnostic sensitivity, when evaluated using spleen samples from mink, and stool samples from mink and foxes. None of the three PCR tests cross-reacted with other parvoviruses. The NS1-probe-PCR also showed a significantly higher specificity than the pan-AMDO-PCR with spleen samples and the best specificity with stool samples. Furthermore, it produced the results more rapidly than the other two PCRs making it a promising tool for both diagnostic and research purposes.
  • Sainio, Markus T.; Aaltio, Juho; Hyttinen, Virva; Kortelainen, Mika; Ojanen, Simo; Paetau, Anders; Tienari, Pentti; Ylikallio, Emil; Auranen, Mari; Tyynismaa, Henna (2022)
    Objectives Clinical diagnostics in adults with hereditary neurological diseases is complicated by clinical and genetic heterogeneity, as well as lifestyle effects. Here, we evaluate the effectiveness of exome sequencing and clinical costs in our difficult-to-diagnose adult patient cohort. Additionally, we expand the phenotypic and genetic spectrum of hereditary neurological disorders in Finland. Methods We performed clinical exome sequencing (CES) to 100 adult patients from Finland with neurological symptoms of suspected genetic cause. The patients were classified as myopathy (n = 57), peripheral neuropathy (n = 16), ataxia (n = 15), spastic paraplegia (n = 4), Parkinsonism (n = 3), and mixed (n = 5). In addition, we gathered the costs of prior diagnostic work-up to retrospectively assess the cost-effectiveness of CES as a first-line diagnostic tool. Results The overall diagnostic yield of CES was 27%. Pathogenic variants were found for 14 patients (in genes ANO5, CHCHD10, CLCN1, DES, DOK7, FKBP14, POLG, PYROXD1, SCN4A, TUBB3, and TTN) and likely pathogenic previously undescribed variants for 13 patients (in genes ABCD1, AFG3L2, ATL1, CACNA1A, COL6A1, DYSF, IRF2BPL, KCNA1, MT-ATP6, SAMD9L, SGCB, and TPM2). Age of onset below 40 years increased the probability of finding a genetic cause. Our cost evaluation of prior diagnostic work-up suggested that early CES would be cost-effective in this patient group, in which diagnostic costs increase linearly with prolonged investigations. Conclusions Based on our results, CES is a cost-effective, powerful first-line diagnostic tool in establishing the molecular diagnosis in adult neurological patients with variable symptoms. Importantly, CES can markedly shorten the diagnostic odysseys of about one third of patients.
  • Lilja, Markus Jukka; Koskinen, Anni; Virkkula, Paula; Vento, Seija Inkeri; Myller, Jyri; Hammaren-Malmi, Sari; Laulajainen-Hongisto, Anu; Hytönen, Maija; Mäkitie, Antti; Numminen, Jura; Sillanpää, Saara; Raitiola, Hannu; Rautiainen, Markus; Toppila-Salmi, Sanna Katriina (2021)
    Objectives: The aim was to compare the control of chronic rhinosinusitis with nasal polyps (CRSwNP) after endoscopic sinus surgery (ESS), in patients with/without nonsteroidal anti-inflammatory drug exacerbated respiratory disease (NERD). Study Desing: A retrospective hospital-based sample of CRSwNP patients with/without NERD with follow-up. Setting: Tertiary rhinology centers. Methods: Electronic patient record data from 116 CRSwNP patients (46 with NERD and 70 without NERD) undergoing ESS during 2001-17 were studied. Mean follow-up time was 9.9 years (range 1.1-15.3). Endpoints reflecting uncontrolled CRSwNP were revision ESS, and need for rescue/advanced therapy (e.g. antibiotics, oral corticosteroids and/or biological therapy) during follow-up. NERD was variable of interest and gender, age, asthma, allergic rhinitis (AR), smoking, Lund-Mackay (LM) score of sinus computed tomography scans previous ESS and baseline total ethmoidectomy were used as covariates. Results: Twenty-one (49.7%) NERD patients and 18 (25.7%) non-NERD patients underwent revision ESS within a mean +/- SD of 4.3 +/- 2.8 and 3.7 +/- 2.6 years, respectively (p = .013, by Logrank test). In Cox ' s regression models, NERD, female gender, young age, asthma, AR, previous ESS, and lack of total ethmoidectomy were associated with revision-ESS. In adjusted model, only the total ethmoidectomy predicted revision-free survival. In adjusted logistic regression model, there was an insignificant trend that NERD and LM score were associated with the need for rescue/advanced therapy in the follow-up. Conclusions: Patients with NERD had higher risk of uncontrolled CRSwNP than patient group without NERD, as measured by revision ESS and/or need for rescue/advanced therapy in the follow-up. In addition, baseline total ethmoidectomy was associated with revision-free survival.
  • Pyöriä, Lari; Jokinen, Maija; Toppinen, Mari; Salminen, Henri; Vuorinen, Tytti; Hukkanen, Veijo; Schmotz, Constanze; Elbasani, Endrit; Ojala, Päivi M.; Hedman, Klaus; Välimaa, Hannamari; Perdomo, Maria F. (2020)
    Infections with the nine human herpesviruses (HHVs) are globally prevalent and characterized by lifelong persistence. Reactivations can potentially manifest as life-threatening conditions for which the demonstration of viral DNA is essential. In the present study, we developed HERQ-9, a pan-HHV quantitative PCR designed in triplex reactions to differentiate and quantify each of the HHV-DNAs: (i) herpes simplex viruses 1 and 2 and varicella-zoster virus; (ii) Epstein-Barr virus, human cytomegalovirus, and Kaposi's sarcoma-associated herpesvirus; and (iii) HHV-6A, -6B, and -7. The method was validated with prequantified reference standards as well as with mucocutaneous swabs and cerebrospinal fluid, plasma, and tonsillar tissue samples. Our findings highlight the value of multiplexing in the diagnosis of many unsuspected, yet clinically relevant, herpesviruses. In addition, we report here frequent HHV-DNA co-occurrences in clinical samples, including some previously unknown. HERQ-9 exhibited high specificity and sensitivity (LOD95 of similar to 10 to similar to 17 copies/reaction), with a dynamic range of 10' to 10 6 copies/p.I. Moreover, it performed accurately in the coamplification of both high- and low-abundance targets in the same reaction. In conclusion, we demonstrated that HERQ-9 is suitable for the diagnosis of a plethora of herpesvirus-related diseases. Besides its significance to clinical management, the method is valuable for the assessment of hitherto-unexplored synergistic effects of herpesvirus coinfections. Furthermore, its high sensitivity enables studies on the human virome, often dealing with minute quantities of persisting HHVs. IMPORTANCE By adulthood, almost all humans become infected by at least one herpesvirus (HHV). The maladies inflicted by these microbes extend beyond the initial infection, as they remain inside our cells for life and can reactivate, causing severe diseases. The diagnosis of active infection by these ubiquitous pathogens includes the detection of DNA with sensitive and specific assays. We developed the first quantitative PCR assay (HERQ-9) designed to identify and quantify each of the nine human herpesviruses. The simultaneous detection of HHVs in the same sample is important since they may act together to induce life-threatening conditions. Moreover, the high sensitivity of our method is of extreme value for assessment of the effects of these viruses persisting in our body and their long-term consequences on our health.
  • van Belkum, Alex; Almeida, Carina; Bardiaux, Benjamin; Barrass, Sarah V.; Butcher, Sarah J.; Çaykara, Tuğçe; Chowdhury, Sounak; Datar, Rucha; Eastwood, Ian; Goldman, Adrian; Goyal, Manisha; Izadi-Pruneyre, Nadia; Jacobsen, Theis; Johnson, Pirjo H.; Kempf, Volkhard A.J.; Kiessling, Andreas; Bueno, Juan Leva; Malik, Anchal; Malmström, Johan; Meuskens, Ina; Milner, Paul A.; Nilges, Michael; Pamme, Nicole; Peyman, Sally A.; Rodrigues, Ligia R.; Rodriguez-Mateos, Pablo; Sande, Maria G.; Silva, Carla Joana; Stehle, Thilo; Thibau, Arno; Vaca, Diana J.; Linke, Dirk (2021)
    Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen-surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin-ligand interaction, supported by present high-throughput "omics" technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
  • Williams, Charles; Palviainen, Mari; Reichardt, Niels-Christian; Siljander, Pia R-M; Falcon-Perez, Juan M. (2019)
    Cell-secreted extracellular vesicles (EVs) have rapidly gained prominence as sources of biomarkers for non-invasive biopsies, owing to their ubiquity across human biofluids and physiological stability. There are many characterisation studies directed towards their protein, nucleic acid, lipid and glycan content, but more recently the metabolomic analysis of EV content has also gained traction. Several EV metabolite biomarker candidates have been identified across a range of diseases, including liver disease and cancers of the prostate and pancreas. Beyond clinical applications, metabolomics has also elucidated possible mechanisms of action underlying EV function, such as the arginase-mediated relaxation of pulmonary arteries or the delivery of nutrients to tumours by vesicles. However, whilst the value of EV metabolomics is clear, there are challenges inherent to working with these entities-particularly in relation to sample production and preparation. The biomolecular composition of EVs is known to change drastically depending on the isolation method used, and recent evidence has demonstrated that changes in cell culture systems impact upon the metabolome of the resulting EVs. This review aims to collect recent advances in the EV metabolomics field whilst also introducing researchers interested in this area to practical pitfalls in applying metabolomics to EV studies.
  • Koskela, Katja A.; Kalin-Manttari, Laura; Hemmila, Heidi; Smura, Teemu; Kinnunen, Paula M.; Niemimaa, Jukka; Henttonen, Heikki; Nikkari, Simo (2017)
    Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus). With the more conventional 16S rDNA PCR analysis, 90 (33%) of the recovered 269 sequence types could be identified to genus level, including Bartonella, Francisella, Mycoplasma, Anaplasma, and Acinetobacter in 31, 15, 9, 9, and 9 sequences, respectively. Seventy-five (28%) matched best with sequences of uncultured bacteria, of which 40/75 could be classified to the order Clostridiales and, more specifically, to families Lachnospiraceae and Ruminococcaceae. Pyrosequencing from 23 samples revealed comparable and similar results: clinically relevant bacterial families such as Mycoplasmataceae, Bartonellaceae, Anaplasmataceae, and Francisellaceae were recognized. These analyses revealed significant bacterial diversity in vole livers, consisting of distinct and constant sequence patterns reflecting bacteria found in the intestinal gut, but including some known zoonotic pathogens as well. The molecular bacterial sequence types determined with the two different techniques shared major similarities and verified remarkable congruency between the methods.
  • Kauffold, Johannes; Peltoniemi, Olli; Wehrend, Axel; Althouse, Gary C. (2019)
    Simply Summary: Real-time ultrasonography (RTU) has become an essential diagnostic value when assessing female swine reproduction in either individual or groups of animals. Diagnostic application of RTU is applied throughout most stages of production, including gilt development, breeding, gestation and farrowing. Along with its most common use in on-farm assessment of pregnancy status, RTU is also used to troubleshoot disruptions in reproductive performance such as delayed puberty, prolonged wean-to-estrus interval, absence of post-weaning estrus, decreased conception and farrowing rates, vulval discharge, peripartum and puerperal disorders. This review aims to provide an overview on principles and clinical uses of RTU in female reproduction on commercial swine farms. Abstract: Within the past 30 years, through ongoing technology and portability developments, real-time (b-mode) ultrasonography (RTU) has increasingly become a valuable diagnostic tool in assessing the female reproductive tract in swine. Initially applied in swine production to visually determine pregnancy status, RTU use has expanded to include assessment of the peri-pubertal and mature non-pregnant females as well. Transabdominal and transrectal modalities to visualizing the reproductive tract in swine have been reported with the transabdominal approach more common due to the fact of its ease of accessibility, animal/personnel safety, and reduced time to perform. Adjustable frequency transducers are preferred as they allow optimization of image quality at various depths. If a single transducer frequency must be selected, a 5 MHz probe provides the best versatility for visualizing the reproductive tract in swine. Other basic requirements for ultrasound equipment which will be used on commercial swine farms include being light weight and easy to handle, readily cleanable and disinfectable, long battery-life, and good durability. When using RTU for pregnancy determination, diagnosis is based upon a combination of the animal's breeding records, the presence of embryonic fluid, and, depending upon gestational stage, fetal structures. If RTU is used as a diagnostic tool in assessing reproductive problems in an individual or a group of animals, sonographic evaluation of both the uterus and ovaries is performed. Tissues are delineated and assessed based upon their echogenicity, echotexture, and size. Uses of RTU in clinical practice may include assessment of delayed puberty, prolonged wean-to-estrus interval, absence of post-weaning estrus, herd disruptions in conception and farrowing rates, vulval discharge, peripartum and puerperal disorders. This review aims to provide an overview on principles and clinical uses of RTU with respect to application to address female reproductive performance issues in commercial swine operations.
  • Loukola, Johanna (Helsingin yliopisto, 2021)
    Cancer is the second leading cause of death worldwide. Cancer is believed to emit volatile organic compounds (VOCs) which dogs may be able to smell. This literature review brings out previous studies about cancer detection dogs, observations made based on them and their future possibilities. There is also some information about training of the dogs, proper test settings and validating a diagnostic test. Detectable odour emissions from a patient with neoplasia, or “smell of cancer”, is an interesting topic, but it has a minor role in this work. Training of the dogs should be done with samples which disease status is confirmed so that the dogs are not rewarded for indicating wrong samples. The trainer must be able to read the dog’s signals and take care of its basic needs in order not to continue training after the dog’s concentration has deteriorated. Training should happen gradually and through positive reinforcement. There should be enough samples and they must not be the same in the testing phase as in training. In validating a diagnostic test, the main goal, materials and methods of the study must be defined and the test should be compared to a golden standard. The smell of cancer is yet unknown although there are studies of the topic. Particular VOCs, which presumably constitute the cancer smell, exist in the body’s secretions. Further studies are needed in order to understand what happens at a molecular level in cancer. There are many studies about cancer detection dogs where they try to discriminate a cancer sample among controls. In these studies, the number of dogs has varied between one to six, there are diverse breeds and dogs have different backgrounds. Good results have been achieved with only two to three weeks of training. Studies have been made of nine different cancer types and the most studied ones have been lung and prostate cancer. Urine and breath were the most common samples used. The sensitivity of cancer odour detecting dogs has varied between 18 to 100%. Previous studies have had different limitations, one of which can be considered having only one cancer sample with controls. This leads to that specificity cannot be held valid. There have been also some limitations in using dogs like short usage time because of their limited life, small number of dogs and wrong rewarding system. There should not be any systematic differences between control and cancer samples including the patient’s age and the handling procedures of samples in the study. Way of life and medications may also have an effect on the dog’s choice, but they were not taken into account in all of the studies. A small number of samples was a problem in some cases. Cancer detection dogs could possibly be used in recognizing the cancer smell, mass screenings, and surveillance after treatments, in addition to laboratory diagnostics and in the developing electronic diagnostic methods such as an artificial nose.
  • Santala, Johanna; Valkonen, Jari P. T. (2018)
    Plants recognize unrelated viruses by the antiviral defense system called RNA interference (RNAi). RNAi processes double-stranded viral RNA into small RNAs (sRNAs) of 21-24 nucleotides, the reassembly of which into longer strands in silico allows virus identification by comparison with the sequences available in databases. The aim of this study was to compare the virus detection sensitivity of sRNA-based virus diagnosis with the established virus species-specific polymerase chain reaction (PCR) approach. Viruses propagated in tobacco plants included three engineered, infectious clones of Potato virus A (PVA), each carrying a different marker gene, and an infectious clone of Potato virus Y (PVY). Total RNA (containing sRNA) was isolated and subjected to reverse-transcription real-time PCR (RT-RT-PCR) and sRNA deep-sequencing at different concentrations. RNA extracted from various crop plants was included in the reactions to normalize RNA concentrations. Targeted detection of selected viruses showed a similar threshold for the sRNA and reverse-transcription quantitative PCR (RT-qPCR) analyses. The detection limit for PVY and PVA by RT-qPCR in this study was 3 and 1.5 fg of viral RNA, respectively, in 50 ng of total RNA per PCR reaction. When knowledge was available about the viruses likely present in the samples, sRNA-based virus detection was 10 times more sensitive than RT-RT-PCR. The advantage of sRNA analysis is the detection of all tested viruses without the need for virus-specific primers or probes.
  • Zhang, Zhen; Douillard, Francois P.; Korkeala, Hannu; Lindstrom, Miia (2022)
    Clostridium botulinum is a notorious pathogen that raises health and food safety concerns by producing the potent botulinum neurotoxin and causing botulism, a potentially fatal neuroparalytic disease in humans and animals. Efficient methods for the identification and isolation of C. botulinum are warranted for laboratory diagnostics of botulism and for food safety risk assessment. The cell wall binding domains (CBD) of phage lysins are recognized by their high specificity and affinity to distinct types of bacteria, which makes them promising for the development of diagnostic tools. We previously identified CBO1751, which is the first antibotulinal phage lysin showing a lytic activity against C. botulinum Group I. In this work, we assessed the host specificity of the CBD of CBO1751 and tested its feasibility as a probe for the specific isolation of C. botulinum Group I strains. We show that the CBO1751 CBD specifically binds to C. botulinum Group I sensu lato (including C. sporogenes) strains. We also demonstrate that some C. botulinum Group I strains possess an S-layer, the disruption of which by an acid glycine treatment is required for efficient binding of the CBO1751 CBD to the cells of these strains. We further developed CBO1751 CBD-based methods using flow cytometry and magnetic separation to specifically isolate viable cells of C. botulinum Group I. These methods present potential for applications in diagnostics and risk assessment in order to control the botulism hazard.
  • Carney, Randy P.; Hazari, Sidhartha; Rojalin, Tatu; Knudson, Alisha; Gao, Tingjuan; Tang, Yuchen; Liu, Ruiwu; Viitala, Tapani; Yliperttula, Marjo; Lam, Kit S. (2017)
    All cells expel a variety of nanosized extracellular vesicles (EVs), including exosomes, with composition reflecting the cells' biological state. Cancer pathology is dramatically mediated by EV trafficking via key proteins, lipids, metabolites, and microRNAs. Recent proteomics evidence suggests that tumor-associated exosomes exhibit distinct expression of certain membrane proteins, rendering those proteins as attractive targets for diagnostic or therapeutic application, yet it is not currently feasible to distinguish circulating EVs in complex biofluids according to their tissue of origin or state of disease. Here, peptide binding to tumor-associated EVs via overexpressed membrane protein is demonstrated. It is found that SKOV-3 ovarian tumor cells and their released EVs express alpha(3)beta(1) integrin, which can be targeted by the in-house cyclic nonapeptide, LXY30. After measuring bulk SKOV-3 EV association with LXY30 by flow cytometry, Raman spectral analysis of laser-trapped single exosomes with LXY30-dialkyne conjugate enables the differentiation of cancer-associated exosomes from noncancer exosomes. Furthermore, the foundation for a highly specific detection platform for tumor-EVs in solution with biosensor surface-immobilized LXY30 is introduced. LXY30 not only exhibits high specificity and affinity to alpha(3)beta(1) integrin-expressing EVs, but also reduces EV uptake into SKOV-3 parent cells, demonstrating the possibility for therapeutic application.