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Klebsiella pneumoniae (K. pneumoniae) is one of the most aggressive multidrug-resistant bacteria associated with human infections, resulting in high mortality and morbidity. We obtained 1190 K. pneumoniae isolates from different patients with urinary tract infections. The isolates were measured to determine their susceptibility regarding nine specific antibiotics. This study's primary goal is to evaluate the potential of infrared spectroscopy in tandem with machine learning to assess the susceptibility of K. pneumoniae within approximately 20 min following the first culture. Our results confirm that it was possible to classify the isolates into sensitive and resistant with a success rate higher than 80% for the tested antibiotics. These results prove the promising potential of infrared spectroscopy as a powerful method for a K. pneumoniae susceptibility test.

Background: Tinea pedis is one of the commonest skin infections of interdigital toe webspace as well as feet skin and may affect the nail or the hand. It is caused by dermophytes fungi especially Trichophyton species. Direct contact with a contaminated environment or animal is the main mode of transmission. Tinea pedis is more frequent among adults than children and more among those with the previous infection with the disease, diabetes mellites, abnormally increased sweating, and the disease is common among individuals who wear unventilated (occlusive) footwear. Tinea pedis is more often in men than females 2-4 times. Aim of the study: To study the epidemiological characteristics and risk factors of tinea pedis disease. Methods: Descriptive study was conducted on patients attending the dermatology outpatient clinic in Tikrit Teaching Hospital, Tikrit, Iraq. The study was done during the period from 1st November 2018-10th June 2019. The sample included (680) persons. The cases were diagnosed clinically and by a direct microscope. The demographic information of patients was obtained according to a certain design questionnaire. The study was done to reveal the epidemiology of tenia pedis disease among affected patients. Results: The frequency of tinea pedis cases among the study sample was (48/ 680) (7%). It has been documented that there is no significant association as a result of the difference in gender, body weight, positive family history, history, presence of fungal skin disease, and presence of nail trauma. Otherwise, there is a significant association as a result of the presence of the young age group, diabetes mellitus, and history of wearing occlusive shoes. Conclusion: The frequency of tinea pedis disease among the study sample was (7%). There was a significant association between age group and the presence of diabetes mellitus disease and wearing occlusive shoes.

Antimicrobial drugs have played an indispensable role in decreasing morbidity and mortality associated with infectious diseases. However, the resistance of bacteria to a broad spectrum of commonly-used antibiotics has grown to the point of being a global health-care problem. One of the most important classes of multi-drug resistant bacteria is Extended Spectrum Beta-Lactamase-producing (ESBL+) bacteria. This increase in bacterial resistance to antibiotics is mainly due to the long time (about 48 h) that it takes to obtain lab results of detecting ESBL-producing bacteria. Thus, rapid detection of ESBL+ bacteria is highly important for efficient treatment of bacterial infections. In this study, we evaluated the potential of infrared microspectroscopy in tandem with machine learning algorithms for rapid detection of ESBL-producing Klebsiella pneumoniae (K. pneumoniae) obtained from samples of patients with urinary tract infections. 285 ESBL+ and 365 ESBL-K. pneumoniae samples, gathered from cultured colonies, were examined. Our results show that it is possible to determine that K. pneumoniae is ESBL+ with ∼89% accuracy, ∼88% sensitivity and ∼89% specificity, in a time span of ∼20 minutes following the initial culture.

Water is the main factor for the healthy life of plant. One of the main negative effects of climate change is the increasing scarcity of water that is lethal for plant. Globally, for water deficit regions (arid and semi-arid), drought is the main factor responsible for low production of agriculture, especially for cotton. Great efforts have been and are being made to find alternatives to water saving practices. This study aimed to examine the effects of partial rhizosphere drying (PRD, half of the root system irrigated at one event, and the other half irrigated in the next event, and so on) with and/or without various mulching treatments on physiological and biochemical traits of cotton. To explore this objective, we laid out experiments in completely randomized design with factorial arrangement in the Islamia University of Bahawalpur, Pakistan in 2016. Two factors included were four mulching treatments (M0, no mulching; M1, black plastic mulching; M2, wheat straw mulching; and M3, cotton sticks mulching) and two irrigation levels (I0, control (full irrigation); and I1, PRD). Fisher’s analysis of variance among means of treatments was compared using least significant difference test at 5% probability level. Results revealed that the maximum plant height, leaf area, leaf gas exchange (photosynthetic rate and stomata conductance), chlorophyll, proline and total sugar contents, and enzyme activities were higher under M2 than under other three mulching treatments. As for irrigation levels, higher values of plant height, photosynthesis and water related parameters (leaf water potential, leaf osmotic potential, leaf turgor potential, etc.) were recorded. Contents of total sugar and proline and activities of antioxidant enzymes were significantly higher in PRD-treated plants than in control plants. It was concluded that combined application of PRD and mulching was more effective than the rest of the treatments used in the experiment. Similar study can be conducted in the field by applying irrigation water in alternate rows in semi-arid regions.

Purpose To evaluate the prevalence and awareness about symptoms, and complications of varicocele among athletes (bodybuilding and aerobics exercises) in Riyadh, Saudi Arabia. Patients and methods A cross-sectional study of male athletes aged between 18 and 48 years old was carried out in multiple branches of fitness centers over a period of 13 months in Riyadh, Saudi Arabia. A total of 382 face-to-face interviews using a predesigned questionnaire were conducted to identify the levels of knowledge, attitude, and practice. A randomly selected 48 subjects were examined. Varicocele was diagnosed and graded based on clinical examination and Doppler ultrasonography. Results Of the participants, 157 (41%) lacked knowledge and awareness regarding varicocele, its symptoms and complications. Of the examined participants, 22 (46%) were found to have varicocele. No difference in varicocele was found among bodybuilders and aerobic athletes (P=0.249). Similarly, no difference was related to duration of exercise session whether for 1 hour or more (P=0.131). However, our study revealed a higher rate of varicocele among athletes who exercised more than three times per week (P=0.009). Testicular volume was neither significantly different among respondents with and without varicocele nor between the left or right sides within each group. Conclusion Knowledge about varicocele, its symptoms and complications is poor among male athletes in Riyadh, Saudi Arabia. Varicocele is more common in athletic men who are frequently exercising. Efforts to increase knowledge and enhance awareness of varicocele in young males, in general, are strongly warranted.

Bacterial infections are significant causes of serious human health problems. Different bacterial pathogens might have similar symptoms, and it is important to detect the cause of the infection early in order to enable effective treatment. In many infections, a mixture of different bacteria might exist in the same tested sample. To treat such infections effectively, it is very important to identify the various types of infecting bacteria in the sample. In this pioneering study, we examined the potential of Fourier transform infrared (FTIR) microscopy for accurate identification and differentiation between different bacteria in experimentally mixed samples of bacteria in the genus level in time span of about 30 min. We have measured the FTIR spectra of bacteria in pure form as well as in various mixtures. Principal components analysis (PCA) was applied on the spectra of various classes, followed by linear discriminant analysis (LDA) as a linear classifier. Our results show that it is possible to differentiate between mixed categories of bacteria with high rates of success. The classification rate was higher when the mixed samples included Gram-positive and Gram-negative types. When the mixing range was comparable ([0.5,0.5] and [0.6,0.4]), a classification success rate > 95% was achieved using only the first 20 PCs.

Bacterial pathogens are one of the primary causes of human morbidity worldwide. Historically, antibiotics have been highly effective against most bacterial pathogens; however, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Early and rapid determination of bacterial susceptibility to antibiotics has become essential in many clinical settings and, sometimes, can save lives. Currently classical procedures require at least 48 h for determining bacterial susceptibility, which can constitute a life-threatening delay for effective treatment. Infrared (IR) microscopy is a rapid and inexpensive technique, which has been used successfully for the detection and identification of various biological samples; nonetheless, its true potential in routine clinical diagnosis has not yet been established. In this study, we evaluated the potential of this technique for rapid identification of bacterial susceptibility to specific antibiotics based on the IR spectra of the bacteria. IR spectroscopy was conducted on bacterial colonies, obtained after 24 h culture from patients' samples. An IR microscope was utilized, and a computational classification method was developed to analyze the IR spectra by novel pattern-recognition and statistical tools, to determine E. coli susceptibility within a few minutes to different antibiotics, gentamicin, ceftazidime, nitrofurantoin, nalidixic acid, ofloxacin. Our results show that it was possible to classify the tested bacteria into sensitive and resistant types, with success rates as high as 85% for a number of examined antibiotics. These promising results open the potential of this technique for faster determination of bacterial susceptibility to certain antibiotics.

Pectobacterium and Dickeya spp. are soft rot Pectobacteriaceae that cause aggressive diseases on agricultural crops leading to substantial economic losses. The accurate, rapid and low-cost detection of these pathogenic bacteria are very important for controlling their spread, reducing the consequent financial loss and for producing uninfected potato seed tubers for future generations. Currently used methods for the identification of these bacterial pathogens at the strain level are based mainly on molecular techniques, which are expensive. We used an alternative method, infrared spectroscopy, to measure 24 strains of five species of Pectobacterium and Dickeya. Measurements were then analyzed using machine learning methods to differentiate among them at the genus, species and strain levels. Our results show that it is possible to differentiate among different bacterial pathogens with a success rate of ~99% at the genus and species levels and with a success rate of over 94% at the strain level.

The spread of multidrug resistant bacteria has become a global concern. One of the most important and emergent classes of multidrug-resistant bacteria is extended-spectrum β-lactamase-producing bacteria (ESBL-positive = ESBL+). Due to widespread and continuous evolution of ESBL-producing bacteria, they become increasingly resistant to many of the commonly used antibiotics, leading to an increase in the mortality associated with resulting infections. Timely detection of ESBL-producing bacteria and rapid determination of their susceptibility to appropriate antibiotics can reduce the spread of these bacteria and the consequent complications. Routine methods used for the detection of ESBL-producing bacteria are time-consuming, requiring at least 48 h to obtain results. In this study, we evaluated the potential of infrared spectroscopic microscopy, combined with multivariate analysis for rapid detection of ESBL-producing Escherichia coli ( E. coli) isolated from urinary-tract infection (UTI) samples. Our measurements were conducted on 837 samples of uropathogenic E. coli (UPEC), including 268 ESBL+ and 569 ESBL-negative (ESBL-) samples. All samples were obtained from bacterial colonies after 24 h culture (first culture) from midstream patients' urine. Our results revealed that it is possible to detect ESBL-producing bacteria, with a 97% success rate, 99% sensitivity, and 94% specificity for the tested samples, in a time span of few minutes following the first culture.

Antimicrobial drugs have an important role in controlling bacterial infectious diseases. However, the increasing resistance of bacteria to antibiotics has become a global health care problem. Rapid determination of antimicrobial susceptibility of clinical isolates is often crucial for the optimal antimicrobial therapy. The conventional methods used in medical centers for susceptibility testing are time-consuming (>2 days). Two bacterial culture steps are needed, the first is used to grow the bacteria from urine on agar plates to determine the species of the bacteria (~24 hours). The second culture is used to determine the susceptibility by growing colonies from the first culture for another 24 hours. Here, the main goal is to examine the potential of infrared microscopy combined with multivariate analysis, to reduce the time it takes to identify Escherichia coli susceptibility to antibiotics and to determine the optimum choice of antibiotic to which the bacteria will respond. E coli colonies of the first culture from patients with urinary tract infections (UTI) were examined for the bacterial susceptibility using Fourier-transform infrared (FTIR). Our results show that it is possible to determine the optimum choice of antibiotic with better than 89% sensitivity, in the time span of few minutes, following the first culture.

Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of receptor-like kinases (RLKs) and play important roles in regulating growth, development, and stress responses in plants. In this study, 246 LRR-RLK genes were identified in the potato (Solanum tuberosum) genome, which were further classified into 14 subfamilies. Gene structure analysis revealed that genes within the same subgroup shared similar exon/intron structures. A signature small peptide recognition motif (RxR) was found to be largely conserved within members of subfamily IX, suggesting that these members may recognize peptide signals as ligands. 26 of the 246 StLRR-RLK genes were found to have arisen from tandem or segmental duplication events. Expression profiling revealed that StLRR-RLK genes were differentially expressed in various organs/tissues, and several genes were found to be responsive to different stress treatments. Furthermore, StLRR-RLK117 was found to be able to form homodimers and heterodimers with StLRR-RLK042 and StLRR-RLK052. Notably, the overlapping expression region of StLRR-RLK117 with Solanum tuberosum WUSCHEL (StWUS) suggested that the CLV3&ndash, CLV1/BAM&ndash, WUS feedback loop may be conserved in potato to maintain stem cell homeostasis within the shoot apical meristem.

Phytophthora infestans (P. infestans) is the causal agent of late blight in potato and tomato. This pathogen devastated the potato crops in Ireland more than a century years ago and is still causing great losses worldwide. Although fungicides controlling P. infestans have been used successfully for almost 100 years, some isolates have developed resistance to most common fungicides. Identification and characterization of these resistant isolates is required for better control of the disease. Current methods that are based on microbiological and molecular techniques are both expensive and time consuming. Fourier Transform Infra-Red spectroscopy (FTIR) is an inexpensive and reagent-free technique that provides accurate results in only a few minutes. In this study the infrared absorption spectra of the sporangia of P. infestans were measured to evaluate the potential of FTIR spectroscopy in tandem with multivariate analysis in order to classify those sporangia into those that were resistant and those that were non-resistant to the phenylamide fungicide mefenoxam. Based on individual measurements, our results show that FTIR spectroscopy enables classification of P. infestans isolates into mefenoxam resistant and mefenoxam non-resistant types with specificity of 81.9% and sensitivity of 75.5%. Using average spectra per leaf, it was possible to improve the classification results to 88% sensitivity and 95% specificity.

Early detection of soil-borne pathogens, which have a negative effect on almost all agricultural crops, is crucial for effective targeting with the most suitable antifungal agents and thus preventing and/or reducing their severity. They are responsible for severe diseases in various plants, leading in many cases to substantial economic losses. In this study, infrared (IR) spectroscopic method, which is known as sensitive, accurate and rapid, was used to discriminate between different fungi in a mixture was evaluated. Mixed and pure samples of Colletotrichum, Verticillium, Rhizoctonia, and Fusarium genera were measured using IR microscopy. Our spectral results showed that the best differentiation between pure and mixed fungi was obtained in the 675–1800 cm−1 wavenumber region. Principal components analysis (PCA), followed by linear discriminant analysis (LDA) as a linear classifier, was performed on the spectra of the measured classes. Our results showed that it is possible to differentiate between mixed-calculated categories of phytopathogens with high success rates (~100%) when the mixing percentage range is narrow (40–60) in the genus level; when the mixing percentage range is wide (10–90), the success rate exceeded 85%. Also, in the measured mixed categories of phytopathogens it is possible to differentiate between the different categories with ~100% success rate.

Bacterial resistance to antibiotics is becoming a global health-care problem. Bacteria are involved in many diseases, and antibiotics have been the most effective treatment for them. It is essential to treat an infection with an antibiotic to which the infecting bacteria is sensitive; otherwise, the treatment is not effective and may lead to life-threatening progression of disease. Classical microbiology methods that are used for determination of bacterial susceptibility to antibiotics are time consuming, accounting for problematic delays in the administration of appropriate drugs. Infrared-absorption microscopy is a sensitive and rapid method, enabling the acquisition of biochemical information from cells at the molecular level. The combination of Fourier transform infrared (FTIR) microscopy with new statistical classification methods for spectral analysis has become a powerful technique, with the ability to detect structural molecular changes associated with resistivity of bacteria to antibiotics. It was possible to differentiate between isolates of Escherichia (E.) coli that were sensitive or resistant to different antibiotics with good accuracy. The objective computational classifier, based on infrared absorption spectra, is highly sensitive to the subtle infrared spectral changes that correlate with molecular changes associated with resistivity. These changes enable differentiating between the resistant and sensitive E. coli isolates within a few minutes, following the initial culture. This study provides proof-of-concept evidence for the translational potential of this spectroscopic technique in the clinical management of bacterial infections, by characterizing and classifying antibiotic resistance in a much shorter time than possible with current standard laboratory methods.

In this study the potential of infrared (IR) spectroscopy for the classification of Colletotrichum coccodes (C. coccodes) isolates into vegetative compatibility groups (VCGs) was evaluated. Isolates which belong to the same VCG may have similar pathological and physiological traits that differ from those that are not assigned to the same VCG. Early classification of isolates into VCGs is of a great importance for a better understanding of the epidemiology of the disease and improves its control. The main goal of the present study was to classify 14 isolates of C. coccodes into VCGs and differentiate between them, based on their IR absorption spectra as obtained by the FTIR-ATR sampling technique. Advanced statistical and mathematical methods, including Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), were applied to the spectra after manipulation. The results show that it is possible to assign the isolates into VCGs with more than 90% success based on the wavenumber low region (1800-800 cm(-1)) and using 15 PCs. However, on the isolate level, the best differentiation results were obtained using PCA (15 PCs) and LDA for the combined regions (2990-2800 cm(-1), 1800-800 cm(-1)), with identification success rates of 87.2%.

Herpes viruses are involved in a variety of human disorders. Herpes Simplex Virus type 1 (HSV-1) is the most common among the herpes viruses and is primarily involved in human cutaneous disorders. Although the symptoms of infection by this virus are usually minimal, in some cases HSV-1 might cause serious infections in the eyes and the brain leading to blindness and even death. A drug, acyclovir, is available to counter this virus. The drug is most effective when used during the early stages of the infection, which makes early detection and identification of these viral infections highly important for successful treatment. In the present study we evaluated the potential of Raman spectroscopy as a sensitive, rapid, and reliable method for the detection and identification of HSV-1 viral infections in cell cultures. Using Raman spectroscopy followed by advanced statistical methods enabled us, with sensitivity approaching 100%, to differentiate between a control group of Vero cells and another group of Vero cells that had been infected with HSV-1. Cell sites that were "rich in membrane" gave the best results in the differentiation between the two categories. The major changes were observed in the 1195-1726 cm(-1) range of the Raman spectrum. The features in this range are attributed mainly to proteins, lipids, and nucleic acids.

Fungi are microorganisms that are divided into groups and subgroups according to their similarity, genera, species, and strains. Fusarium is considered a phytopathogen that attacks variety of crops throughout the world, causing diseases resulting in severe economic losses. Many of the Fusarium species cause similar symptoms, making it impossible to distinguish among them based on symptoms alone. Fungicides are commonly the most effective treatment of these pathogens, and their use is effective and could prevent or decrease its severity and spread when detected early. Currently, classical methods (microbiological, molecular) are time-consuming. In this study, we aimed to distinguish among three different groups: Fusarium oxysporum, Fusarium solani, and a mixture of both species. Thus, we used Fourier transform infrared microscopy combined with principal component analysis (PCA) and linear discriminant analysis (LDA) classifier. Using the first ten PCs, our classification results showed a 94% success rate in distinguishing among the three groups.

Of the eight members of the herpes family of viruses, HSV1, HSV2, and varicella zoster are the most common and are mainly involved in cutaneous disorders. These viruses usually are not life-threatening, but in some cases they might cause serious infections to the eyes and the brain that can lead to blindness and possibly death. An effective drug (acyclovir and its derivatives) is available against these viruses. Therefore, early detection and identification of these viral infections is highly important for an effective treatment. Raman spectroscopy, which has been widely used in the past years in medicine and biology, was used as a powerful spectroscopic tool for the detection and identification of these viral infections in cell culture, due to its sensitivity, rapidity and reliability. Our results showed that it was possible to differentiate, with a 97% identification success rate, the uninfected Vero cells that served as a control, from the Vero cells that were infected with HSV-1, HSV-2, and VZV. For that, linear discriminant analysis (LDA) was performed on the Raman spectra after principal component analysis (PCA) with a leave one out (LOO) approach. Raman spectroscopy in tandem with PCA and LDA enable to differentiate among the different herpes viral infections of Vero cells in time span of few minutes with high accuracy rate. Understanding cell molecular changes due to herpes viral infections using Raman spectroscopy may help in early detection and effective treatment.

Intermediate filament (IF) proteins are known mainly by their propensity to form viscoelastic filamentous networks within cells. In addition, IF-proteins are essential parts of various biological materials, such as horn and hagfish slime threads, which exhibit a range of mechanical properties from hard to elastic. These properties and their self-assembly nature made IF-proteins attractive building blocks for biomimetic and biological materials in diverse applications. Here we show that a type V IF-protein, the Caenorhabditis elegans nuclear lamin (Ce-lamin), is a promising building block for protein-based fibers. Electron cryo-tomography of vitrified sections enabled us to depict the higher ordered assembly of the Ce-lamin into macroscopic fibers through the creation of paracrystalline fibers, which are prominent in vitro structures of lamins. The lamin fibers respond to tensile force as other IF-protein-based fibers, i.e., hagfish slime threads, and possess unique mechanical properties that may potentially be used in certain applications. The self-assembly nature of lamin proteins into a filamentous structure, which is further assembled into a complex network, can be easily modulated. This knowledge may lead to a better understanding of the relationship in IF-proteins-based fibers and materials, between their hierarchical structures and their mechanical properties.

Fungi are considered as serious pathogens for many plants, potentially causing severe economic damage. Early detection and identification of these pathogens is crucial for their timely control. The methods available for identification of fungi are time consuming and not always very specific. In this study, the potential of FTIR-ATR spectroscopy was examined together with advanced mathematical principle component analysis (PCA) and statistical linear discriminant analysis (LDA) to differentiate among 10 isolates of Fusarium oxysporum. The results are encouraging and indicate that FTIR-ATR can successfully detect different isolates of Fusarium oxysporum. Based on PCA and LDA calculations in the region 850–1775 cm-1with 16 PC's, the different strains from the same fungal genus could be classified with 75.3% and 69.5% success rates using the “leave one out” method and “20–80% algorithm” respectively.

Fourier Transform Infrared (FTIR) and Raman spectroscopies have emerged as powerful tools for chemical analysis. This is due to their ability to provide detailed information about the spatial distribution of chemical composition at the molecular level. A biological sample, i.e. bacteria or fungi, has a typical spectrum. This spectral fingerprint, characterizes the sample and can therefore be used for differentiating between biology samples which belong to different groups, i.e., several different isolates of a given fungi. When the spectral differences between the groups are minute, multivariate analysis should be used to provide a good differentiation. We hereby review several results which demonstrate the differentiation success obtained by combining spectroscopy measurements and multivariate analysis.

Fourier transform infrared (FTIR) spectroscopy is a unique technique for the laboratory diagnosis of cellular variations based on the characteristic molecular vibrational spectra of the cells. Microscopic FTIR was used to investigate spectral differences between normal and malignant fibroblasts transformed by retrovirus infection. A detailed analysis showed significant differences between cancerous and normal cells. The contents of vital cellular metabolites were significantly lower in the transformed cells than in the normal cells. In an attempt to identify the cellular components responsible for the observed spectral differences between normal and cancerous cells, we found significant differences between DNA of normal and cancerous cells.

Background Cancer is one of the leading worldwide causes of death. It may be induced by a variety of factors, including carcinogens, radiation, genetic factors, or DNA and RNA viruses. The early detection of cancer is critical for its successful therapy, which can result in complete recovery from some types of cancer. Methods Raman spectroscopy has been widely used in medicine and biology. It is a noninvasive, nondestructive, and water-insensitive technique that can detect changes in cells and tissues that are caused by different disorders, such as cancer. In this study, Raman spectroscopy was used for the identification and characterization of murine fibroblast cell lines (NIH/3T3) and malignant fibroblast cells transformed by murine sarcoma virus (NIH-MuSV) cells. Results Using principal component analysis and LDA it was possible to differentiate between the NIH/3T3 and NIH-MuSV cells with an 80–85% success rate based on their Raman shift spectra. Conclusions The best results for differentiation were achieved from spectra that were obtained from the rich membrane sites. General significance Because of its homogeneity and complete control of most factors affecting its growth, cell culture is a preferred model for the detection and identification of specific biomarkers related to cancer transformation or other cellular modifications.

Cancer diagnosis using infrared spectroscopy uses absorbance of nucleic acids, carbohydrates and phosphates as biomarkers. The present work deciphers the mutual intereference in absorbance of these compnents using colonic tissues as a model.

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus which causes anthracnose on tomatoes and black dot disease in potatoes. It is important to differentiate among these isolates and to detect the origin of newly discovered isolates, in order to treat the disease in its early stages. However, distinguishing between isolates using common biological methods is time-consuming, and not always available. We used Fourier Transform Infra-Red (FTIR)-Attenuated Total Reflectance (ATR) spectroscopy and advanced mathematical and statistical methods to distinguish between different isolates of C. coccodes. To our knowledge, this is the first time that FTIR-ATR spectroscopy was used, combined with multivariate analysis, to classify such a large number of 15 isolates belonging to the same species. We obtained a success rate of approximately 90% which was achieved using the region 800-1775 cm(-1). In addition we succeeded in determining the relative spectral similarity between different fungal isolates by developing a new algorithm. This method could be an important potential diagnostic tool in agricultural research, since it may outline the extent of the biological similarity between fungal isolates. Based on the PCA calculations, we grouped the fifteen isolates included in this study into four different degrees of similarity.

The early diagnosis of phytopathogens is of a great importance; it could save large economical losses due to crops damaged by fungal diseases, and prevent unnecessary soil fumigation or the use of fungicides and bactericides and thus prevent considerable environmental pollution. In this study, 18 isolates of three different fungi genera were investigated; six isolates of Colletotrichum coccodes, six isolates of Verticillium dahliae and six isolates of Fusarium oxysporum. Our main goal was to differentiate these fungi samples on the level of isolates, based on their infrared absorption spectra obtained using the Fourier transform infrared-attenuated total reflection (FTIR-ATR) sampling technique. Advanced statistical and mathematical methods: principal component analysis (PCA), linear discriminant analysis (LDA), and k-means were applied to the spectra after manipulation. Our results showed significant spectral differences between the various fungi genera examined. The use of k-means enabled classification between the genera with a 94.5% accuracy, whereas the use of PCA [3 principal components (PCs)] and LDA has achieved a 99.7% success rate. However, on the level of isolates, the best differentiation results were obtained using PCA (9 PCs) and LDA for the lower wavenumber region (800-1775 cm(-1)), with identification success rates of 87%, 85.5%, and 94.5% for Colletotrichum, Fusarium, and Verticillium strains, respectively.

Conventional synthesis of silver nanoparticles employs a reducing agent and a capping agent. In this report water-soluble silver nanoparticles (AgNPs) were prepared facilely by chemical reduction of Ag(I) ions. 4-Amino-3-( d -gluco-pentitol-1-yl)-4,5-dihydro-1,2,4-triazole-5-thione (AGTT) was used both as reducing and stabilizing agent. Direct heating methodology was found to be more suitable for achieving particles with a hydrodynamic diameter of ∼20 nm. AGTT exists as tautomer in solution form and our studies indicate that –NH2 group is involved in the reduction and stabilization of Ag+ and thione (Δ=S) group of AGTT is possibly involved in stabilizing the nanoparticles via coordinate covalent linkage. Characterization of synthesized silver nanoparticles was performed by UV–vis, FT-IR and by FESEM. Based on the absorption properties of synthesized AgNPs, we used AgNPs to detect bovine serum albumin (BSA) and AgNPs-BSA composite nanoprobe was further applied to detect Cu2+ based on absorbance recovery. The proposed method has advantages over existing methods in terms of rapid synthesis and stability of AgNPs and their applications. Analysis is reproducible, cost effective and highly sensitive. The lowest detectable concentration of BSA in this approach is 3 nM, and for Cu2+ it can detect upto 200 pM.

Fusarium is a large fungi genus of a large variety of species and strains which inhabits soil and vegetation. It is distributed worldwide and affiliated to both warm and cold weather. Fusarium oxysporum species, for instance, cause the Fusarium wilt disease of plants, which appears as a leaf wilting, yellowing and eventually plant death. Early detection and identification of these pathogens are very important and might be critical for their control. Previously, we have managed to differentiate among different fungi genera (Rhizoctonia, Colletotrichum, Verticillium and Fusarium) using FTIR-ATR spectroscopy methods and cluster analysis. In this study, we used Fourier-transform infrared (FTIR) attenuated total reflection (ATR) spectroscopy to discriminate and differentiate between different strains of F. oxysporum. The result obtained was of spectral patterns distinct to each of the various examined strains, which belong to the same species. These differences were not as significant as those found between the different genera species. We applied advanced statistical techniques: principal component analysis (PCA) and linear discriminant analysis (LDA) on the FTIR-ATR spectra in order to examine the feasibility of distinction between these fungi strains. The results are encouraging and indicate that the FTIR-ATR methodology can differentiate between the different examined strains of F. oxysporum with a high success rate. Based on our PCA and LDA calculations performed in the regions [900–1775 cm−1, 2800–2990 cm−1, with 9 PCs], we were able to classify the different strains with high success rates: Foxy1 90%, Foxy2 100%, Foxy3 100%, Foxy4 92.3%, Foxy5 83.3% and Foxy6 100%.

FTIR spectroscopy has been extensively used to understand the differences between normal and malignant cells and tissues. In the present study, FTIR microspectroscopy was performed on biopsies to evaluate parameters deduced from changes in nucleic acid absorbance monitored at various characteristic wavenumbers in the Mid-IR region. The data showed that there were differences in the spectra of normal and malignant tissues from several organs such as colon, cervix, skin and blood with respect to absorbance due to nucleic acids. Similar results were observed in the case of cell lines that were transformed to induce carcinogenesis. Of the several ratios examined for consistency in differentiating cancer and normal tissues, the I(996 cm−1)/I(966 cm−1) showed promise as a distinguishing parameter and was comparable to the I(1121 cm−1)/I(1020 cm−1) ratio reported in many earlier studies. The absorbance of nucleic acids is presented with an emphasis on the application of FTIR microspectroscopy for diagnosis of malignancy. Our results indicate that usage of nucleic acid absorbance yield statistically significant parameters, which could differentiate normal and cancerous tissues.

Abnormal crypt proliferation and development in the colon has been associated with premalignant stages of colon cancer. Conventionally, molecular markers are used to detect abnormal crypt proliferation.In the present work, feasibility studies of FTIR-MSP to distinguish between normal and abnormal crypts from colon biopsies that show normal histopathological features have been undertaken.The results indicate that abnormal crypts show deviations in the pattern of absorbance in the Mid IR region along the crypt height when compared with the normal crypts. The crypts could be empirically classified into three groups such as crypts having a normal absorbance pattern for all biochemical components, crypts with abnormal absorbance pattern for some biochemical components and crypts with completely abnormal absorbance pattern along the height for all or most biochemical components studied by FTIR. The utilization of FTIR-MSP is proposed for diagnosis of abnormal metabolism at the molecular level of histologically completely normal-looking crypts, especially from those biopsies that are taken from sites far away from cancer.This method could give rise to a reduction in false-negative results during examination of biopsies using the conventional histopathological methods. The present method may be complementary to existing methods for precise demarcation of the zone of colostomy prior to colon cancer surgery.

Fourier transform infrared microspectroscopy (FTIR-MSP), which is based on the characteristic molecular vibrational spectra of cells, was used to investigate spectral differences between normal primary rabbit bone marrow (BM) cells and bone marrow cells transformed (BMT) by murine sarcoma virus (MuSV). Primary cells, rather than cell lines, were used for this research because primary cells are similar to normal tissue cells in most of their characteristics. Our results showed dramatic changes in absorbance between the control cells and MuSV124-transformed cells. Various biological markers, such as the phosphate level and the RNA/DNA obtained, based on the analysis of the FTIR-MSP spectra, also displayed significant differences between the control and transformed cells. Preliminary results suggested that the cluster analysis performed on the FTIR-MSP spectra yielded 100% accuracy in classifying both types of cells.

The intestinal crypts contain mucus-secreting goblet cells in large numbers. In the tubular gland (crypt), the cells are generated at the bottom and end their life cycle at the top. Recently, FTIR microspectroscopy (FTIR-MC) has been applied in biology and medicine. The characterization of various cellular types using FTIR-MC and its subsequent application for the diagnosis of cancer is becoming a reality. In this report, we investigate the differential cellular activity in the normal tubular gland using FTIR-MC. Our results indicate that the absorbance for the cells in the bottom of the crypt is always higher than those in the upper portion. There are spectral pattern changes and frequency shifts for cells at the bottom and top sites of the normal crypt. Also, the comparison of a normal crypt with a malignant one has been made. This is the first spectroscopic evidence in the literature showing the difference in the cellular activity at different sites in the tubular gland. The reasons for our observations and their implications are discussed.

Autofluorescence from intracellular chromophores upon illumination of cells by monochromatic light has been studied towards the development of novel noninvasive and sensitive technology for the early detection of cancer. To investigate the relationship between biochemical and morphological changes underlying malignant disease and resulting fluorescence spectra, an in vitro model system of a paired normal and malignant murine fibroblasts cell lines, differing in cancer-associated H-ras expression was employed. A comparison of fluorescence excitation and emission spectra of proliferative cells revealed that fluorescence intensity of malignant cells was significantly less than that of normal cells upon excitation at 290 nm. Fluorescence of both cell lines decreased with decreasing cell concentration, but at each concentration, normal cells had higher fluorescence intensity than malignant cells. Similar differences between the cell lines were observed when brought to quiescence or at stationary phase. Results suggested that the chromophore contributing most significantly to these spectra is tryptophan and its moieties in proteins. This model system demonstrates the specific contribution of H-ras to subcellular chromophores, resulting in a significant difference in their autofluorescence intensity, and implies the potential use of the technique for cancer detection. This model system is potent for analysis of the contribution of other oncogenes and their combinations towards spectral detection of cancer.

Recently, microscopic FTIR is widely used in the field of biology and medicine. FTIR can detect biomolecular changes in the cells and tissues responsible for various disorders. In this report, we characterize the H-ras transfected fibroblasts and its normal control using microscopic FTIR. The intensity of the normal fibroblasts was higher than that of H-ras transfected fibroblasts. Our studies showed significant differences occur in the concentration of vital metabolites upon transformation. The DNA and carbohydrates level decreased in the transformed cells compared to the controls. A linear correlation could be found between the levels of carbohydrates and phosphate, while the RNA/DNA ratio varied inversely with glucose/phosphate levels.

Light-induced Fluorescence (LIF) technique is based on fluorescence emitted from intracellular chromophores upon illumination of cells by monochromatic light. We compared LIF emitted from a pair of normal and malignant murine cell lines, differing in H-ras expression. The malignant cells fluoresced significantly less than the normal cells, upon excitation at 290 +/- 10 nm. For both cell types, fluorescence decreased with decreasing cell concentration, but at each concentration, the normal cells fluoresced more than the malignant cells. The effect of viability and metabolic stage of the cells on this pattern was compared. The difference among the cells was not due to a difference in protein or DNA content. Thus, this model system demonstrates the specific contribution of H-ras to sub-cellular chromophores, resulting in a significant difference in their autofluorescence intensity, while measuring both emission and excitation scans. This study suggests a potential use of the LIF technique to distinguish between normal and malignant cells and tissues.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.