Microbiology and Molecular Biology

Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A t...

ABSTRACT

It has been established that the symbiosis between Rhizobium and legumes are a cheaper and usually more effective agronomic practice for ensuring an adequate supply of nitrogen for legume based crop and pasture production than the application of nitrogen fertilizer. Crolotalaria ocroleuca is one of the members of crotalaria grown as cover crop or inter crop in southern and south western parts of Ethiopia.  Nineteen isolates were isolated from the root nodules of Crolotalaria ocroleuca from coffee growing area in Godere Wereda, Gambella region under Teppi Coffee plantation Enterprise. Presumptive tests and microscopic features confirmed that the isolates were rod shaped and gram-negative rhizobia. Based on colony and growth characters the isolates were grouped into two groups.    Accordingly, 15 isolates were fast growing and acid producing Rhizobium spp; whereas four isolates (AAUCR4.AAUCR9, AAUCR14 and AAUCR18) were slow growing and alkali producing Brady rhizobium spp. Most of the isolates utilized the carbohydrates; sorbitol, xylose, and lactose, whereas only 26% and 15% were able to utilize starch and Na-citrate, respectively. All isolates were resistant to kanamycin and erythromycin at lower concentration of 2.5 and 5 µm/ml. Only 68% and 79% were résistance at (2.5 µm/ml) and 63% and 16% of the isolates were resistant at (5 µm/ml) to neomycin and gentamycin, respectively whereas isolates (AAUCR9 and AAUCR18) were resistant to all the tested antibiotics. The isolates also showed variability in their physiological characteristics. All isolates grew at 300C .while, 63% and 53% of the isolates were able to tolerate 150C and 400C respectively. All isolates were able to grow at lower salt concentration (1-2%), and five isolates (26%) showed tolerance up to 4%. Only isolate (AAUCR9) was considered highly osmo-tolerant since it grew at 5% of salt concentration.  Amongst the isolates, 21% were able to form clear zones around their colonies on Pikovaskaya’s medium and hence, they were considered as phosphate solubilisers with solubilisation index ranging from (2.2 -3). Relative effectiveness of the isolates was calculated by dry mass of the inoculated plant over the dry mass of positive control has significant difference within and among the treatment and positive and negative control at (p<0.05 Tukey’s test HSD) and accordingly, 47%, and 32%, of the isolates (79%) were highly effective (80-100%), and effective (50-80%) in nitrogen fixation. Generally, with over all competency analysis measurement two isolates AAUCR9 and AAUCR18 were the best isolates in terms of effective nitrogen fixation and tolerance to various ecological features that could make them competent against prospective candidates under field conditions.
Key words:  cultural characters; Gambella; IAR; pH tolerance; symbiotic effectiveness.

Phenylhydrazine (PHZ), a potent chemical causes toxicity on various tissues at various levels. Administration of phenylhydrazine mainly causes haematotoxicity which leads to the haemolytic anemia. In mammals PHZ induced anemia increased the iron absorption in spleen, liver and duodenum and finally iron metabolism was altered. Local demand and supply of Fe would increase erythropoeitic activity of the spleen so the size of spleen was increased that create the splenomegaly. PHZ induced anemia activate immune response which triggers phagocytosis in the spleen and liver. Apart from this administration of PHZ interfere the binding of erythropoietin (EPO) with erythropoietin receptors (EPOR) so that JAK-STAT would be affected.PHZ also showed genotoxic effect by creating single strand DNA damage.

The present study aimed to the occurrence of mycoflora in poultry feed, determination of aflatoxigenic Aspergillus flavus and compatible homology aflatoxigenic A.flavus strains with other strains in gene bank. A total of 180 samples of concentrated poultry feed pellet were collected from different broilers, broiler breeders and layers farms and local market of poultry in Basrah province . Feed samples were collected during the period from Sep. 2014 to Apr. 2015. About 10 - 30 representative samples of 1 kg were collected from several locations. They were cultured on Potato dextrose agar(PDA) and malt extract agar (MEA) and then subcultured on Sabouraud dextrose agar (SDA) and coconut medium agar(CAM) .Seven genera were recovered from 180 samples of poultry feed .The most genera which recovered were Aspergillus (frequency(Fr) 62.77% - Relative density(RD) 52.03%), followed by Penicillium (Fr 47.77% - RD 17.01%) were the predominant genera isolated from poultry feed, while Fusarium isolates were less frequency and relative density(Fr.1.66%, RD 2.11%) .The most frequently isolated Aspergillus spp.was Aspergillys flavus ( Fr 65.48%) and had the most RD (27.55%) , followed by A.niger (Fr. 58.40%, RD14.23%),the less occurrence of Aspergillus was A.paraciticus(Fr.1.76%, RD0.89%) .Fifty isolates of A. flavus were detect by UV light (365nm) and ammonia vapor to detect aflatoxigenic A.flavus on CAM by colored with blue –green on reverse of glass petri dish under UV light and produce a pink to red color by exposure to ammonia vapor. The detection by fluorescent blue revealed that 26 (52%) of isolates were aflatoxigenic (positive)by produce
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fluorescent color under UV (356nm) light , and also 26 (52%) of isolates were aflatoxigenic (positive) by ammonia vapor test. The molecular assessment was done on 50 isolates of A.flavus by using primers pair for the aflatoxin regulatory gene aflR in polymerase chain reaction (PCR). Five isolates of aflatoxigenic A. flavus positive identified isolates by PCR were randomly selected to sequence and analyze by basic local alignment search tool analysis (BLAST) to confirm the aflatoxigenic strains. Five isolates were positive and confirmed approximately compatible(100% and 99%) homology with other A.flavus strains on NCBI .

For thousands of years, microorganisms have been used to supply products such as bread, beer and wine. Asecond phase of traditional microbial biotechnology began during World War I and resulted in the development of the acetone-butanol and glycerol fermentations,
followed by processes yielding, for example, citric acid, vitamins and antibiotics. In the early 1970s, traditional industrial microbiology was merged with molecular biology to yield more than 40 biopharmaceutical products, such as erythropoietin, human growth hormone and
interferons. Today , microbiology is a major participant in global industry , especially in the pharmaceutical, food and chemical industries.

The budding yeast Saccharomyces cerevisiae has been the principal organism used in experiments to examine genetic recombination in eukaryotes. Studies over the past decade have shown that meiotic recombination and probably most mitotic recombination arise from the repair of double-strand breaks (DSBs). There are multiple pathways by which such DSBs can be repaired, including several homologous recombination pathways and still other nonhomologous mechanisms. Our understanding has also been greatly enriched by the characterization of many proteins involved in recombination and by insights that link aspects of DNA repair to chromosome replication. New molecular models of DSB-induced gene conversion are presented. This review encompasses these different aspects of DSB-induced recombination in Saccharomyces and attempts to relate genetic, molecular biological, and biochemical studies of the processes of DNA repair and recombination.

Background: There are no robust national prevalence of Human Papillomavirus (HPV) genotypes in Nigerian women despite the high burden of cervical cancer morbidity and mortality. The objective of study: This study aims to determine the pooled prevalence and risk factors of genital HPV infection in Nigeria through a systemic review protocol. Methods: Databases including PubMed, Scopus, Google Scholar and AJOL were searched between 10 April to 28 July 2020. HPV studies on Nigerian females and published from April 1999 to March 2019 were included. GRADE was used to assess the quality of evidence. Results: The pooled prevalence of cervical HPV was 20.65% (95%CI: 19.7-21.7). Genotypes 31 (70.8%), 35 (69.9%) and 16 (52.9%) were the most predominant HPV in circulation. Of the six geopolitical zones in Nigeria, northeast had the highest pooled prevalence of HPV infection (48.1%), while the least was in the northwest (6.8%). After multivariate logistic regression, duration (years) of sexual exposure (OR ¼ 3.24, 95%CI: 1.78-9.23]), history of other malignancies (OR ¼ 1.93, 95%CI: 1.03-2.97]), history of sexually transmitted infection (OR ¼ 2.45, 95% CI: 1.31-3.55]), coital frequency per week (OR ¼ 5.11, 95%CI: 3.86-14.29), the status of circumcision of the sexual partner (OR ¼ 2.71, 95%CI: 1.62-9.05), and marital status (OR ¼ 1.72, 95%CI: 1.16-4.72), were significant risk factors of HPV infection (p < 0.05). Irregular menstruation, postcoital bleeding and abdominal vaginal discharge were significantly associated with HPV infection (p < 0.05). Conclusion: HPV prevalence is high in Nigeria and was significantly associated with several associated risk factors. Rapid screening for high-risk HPV genotypes is recommended and multivalent HPV vaccines should be considered for women.

Objective: To elucidate the capabilities of carboxy methyl cellulase (CMCase) production with the selective species of Aspergillus flavus (A. flavus). Methods: The carboxy methyl cellulase (CMCase) expression in A. flavus was evaluated under different environmental conditions using submerged fermentation (SmF) on different agricultural byproducts. Results: A. flavus produced high levels of CMCase under optimized culture conditions on 3rd day of incubation at an optimum pH 6.0, temperature 30 曟, inoculum size 4% in Czapek Dox using wheat bran as a substrate by SmF. Enhanced production occurred on addition of 4% wheat bran and 1% peptone as nutritional factors. The enzyme hydrolyzed wheat bran exhibiting Vmax value of 40 U/mg and K m value of 0.5 mg/mL at pH of 7. The enzyme was optimally activated 50 曟. Except Mg2+, all other metal ions such as Zn2+, Cu2+, Na+ and Ca2+ were found to be activators for the enzyme activity.Conclusion: The kinetic parameters showed the thermo stability, pH stability of the enzyme which reflects the potential and commercial significance of the enzyme.

Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not co...

Human papillomaviruses (HPV) are the etiological agents of cervical and other anogenital malignancies. Over 100 different types of HPVs have been identified to date, and all target epithelial tissues for infection. One-third of HPV types specifically infect the genital tract, and a subset of these are the causative agents of anogenital cancers. Other HPV types that infect the genital tract induce benign hyperproliferative lesions or genital warts. The productive life cycle of HPVs is linked to epithelial differentiation. Papillomaviruses are thought to infect cells in the basal layer of stratified epithelia and establish their genomes as multicopy nuclear episomes. In these cells, viral DNA is replicated along with cellular chromosomes. Following cell division, one of the daughter cells migrates away from the basal layer and undergoes differentiation. In highly differentiated suprabasal cells, vegetative viral replication and late-gene expression are activated, resulting in the generation of progeny virions. Since virion production is restricted to differentiated cells, infected basal cells can persist for up to several decades or until the immune system clears the infection. The E6 and E7 genes encode viral oncoproteins that target Rb and p53, respectively. During the viral life cycle, these proteins facilitate stable maintenance of episomes and stimulate differentiated cells to reenter the S phase. The E1 and E2 proteins act as origin recognition factors as well as regulators of early viral transcription. The functions of the E5 and E1--E4 proteins are still largely unknown, but these proteins have been implicated in modulating late viral functions. The L1 and L2 proteins form icosahedral capsids for progeny virion generation. The characterization of the cellular targets of these viral proteins and the mechanisms regulating the differentiation-dependent viral life cycle remain active areas for the study of these important human pathogens.

BACKGROUND: Cryptococcus neoformans is responsible of cryptococcosis, a life-threatening infection that affects healthy and immunocompromised individuals. It is the first cause of adult acute meningitis in some sub-Saharan African countries with a mortality rate of about 100% in cases of inappropriate therapy. This study aimed at examining the occurrence and the antifungal patterns of Cryptococcus isolates from pigeon droppings and bat guanos in the west region of Cameroon. METHODS: A total of 350 samples were randomly collected from three selected localities of west region of Cameroon. The identification was performed based on capsule production assessed by Indian ink preparation. Additional tests performed were urea broth, glycine and tryptophan assimilation tests. The antifungal susceptibility test was performed by the broth microdilution method. RESULTS: Mycological analysis led to the identification of 98 isolates, of which 57 isolates of C. neoformans var. gattii and 41 isolates of C. neoformans var. neoformans. All the isolates showed resistance to antifungals tested except nystatin which showed MIC mean values ranging between 0.5 µg/mL and 0.65 µg/mL. CONCLUSION: The prevalence of C. neoformans in pigeons and bats excreta in the west region of Cameroon is 28.57 %. C. neoformans var. gattii and C. neoformans var. neoformans are the main serotypes. Isolates found to be resistant to fluconazole and ketoconazole. Our results emphasize the need for further study on the molecular epidemiology in comparison with clinical isolates.

There is ample evidence that cells of higher eukaryotes express double-stranded RNA molecules (dsRNAs) either naturally or as the result of viral infection or aberrant, bidirectional transcriptional readthrough. These duplex molecules can exist in either the cytoplasmic or nuclear compartments. Cells have evolved distinct ways of responding to dsRNAs, depending on the nature and location of the duplexes. Since dsRNA molecules are not thought to exist naturally within the cytoplasm, dsRNA in this compartment is most often associated with viral infections. Cells have evolved defensive strategies against such molecules, primarily involving the interferon response pathway. Nuclear dsRNA, however, does not induce interferons and may play an important posttranscriptional regulatory role. Nuclear dsRNA appears to be the substrate for enzymes which deaminate adenosine residues to inosine residues within the polynucleotide structure, resulting in partial or full unwinding. Extensively modifi...

The use of antibiotics for prophylaxis and growth enhancement in livestock farming is on the increase globally. This practice has led to the emergence and spread of antimicrobial-resistant bacteria in livestock. Only limited research has been done to establish the role of cattle farming in antimicrobial resistance. The current study sought to establish the carriage of multi-drug resistance and extended-spectrum beta-lactamase genes in Escherichia coli from farmers, their cattle, and cattle slurry within Kiambu County. A total of 286 (81%) E. coli isolates were recovered from 352 samples analysed. Antibiotic resistance profiles showed 114 (40%) isolates were resistant to ≥3 antimicrobial classes and were considered multidrug-resistant. Among multidrug-resistant (MDR) E. coli strains, 40 (14%) were resistant to 3 different antimicrobial classes, while 71 (25%) were resistant to between 4 and 7 antibiotic classes. Extended-spectrum β-lactamase resistance was found in 18 isolates: human (n = 14), cattle (n = 2), and environmental (n = 2). Both the blaCTX-M and blaTEM genes were detected in 10 and 15 strains, respectively. Sequence analysis showed that the isolates carried the blaTEM-116 (n = 7), blaTEM-1 (n = 5), and blaCTX-M-15 (n = 8) genes. Genotyping MDR isolates using (GTG) 5 PCR demonstrated that the isolates were not clonal. This data shows antimicrobial resistance profiles and different types of resistance genes in the E. coli population on dairy farms. As a result, more effective, targeted public health policies and measures need to be put in place to control and prevent the emergence and spread of resistant bacteria.

Frankia strains are N2-fixing actinomycetes whose isolation and cultivation were first reported in 1978. They induce N2-fixing root nodules on diverse nonleguminous (actinorhizal) plants that are important in ecological successions and in land reclamation and remediation. The genus Frankia encompasses a diverse group of soil actinomycetes that have in common the formation of multilocular sporangia, filamentous growth, and nitrogenase-containing vesicles enveloped in multilaminated lipid envelopes. The relatively constant morphology of vesicles in culture is modified by plant interactions in symbiosis to give a diverse array of vesicles shapes. Recent studies of the genetics and molecular genetics of these organisms have begun to provide new insights into higher-plant-bacterium interactions that lead to productive N2-fixing symbioses. Sufficient information about the relationship of Frankia strains to other bacteria, and to each other, is now available to warrant the creation of some...

Changes in public opinion and legislation have led to the general recognition that solid waste treatment practices must be changed. Solid-waste disposal by landfill is becoming increasingly expensive and regulated and no longer represents a long-term option in view of limited land space and environmental problems. Yard waste, a significant component of municipal solid waste, has previously not been separated from the municipal solid-waste stream. The treatment of municipal solid waste including yard waste must urgently be addressed because disposal via landfill will be prohibited by legislation. Separation of yard waste from municipal solid waste will be mandated in many localities, thus stressing the importance of scrutinizing current composting practices in treating grass clippings, leaves, and other yard residues. Yard waste poses a potential environmental health problem as a result of the widespread use of pesticides in lawn and tree care and the persistence of the residues of t...

SUMMARY The processes that govern the regulated transport of long-chain fatty acids across the plasma membrane are quite distinct compared to counterparts involved in the transport of hydrophilic solutes such as sugars and amino acids. These differences stem from the unique physical and chemical properties of long-chain fatty acids. To date, several distinct classes of proteins have been shown to participate in the transport of exogenous long-chain fatty acids across the membrane. More recent work is consistent with the hypothesis that in addition to the role played by proteins in this process, there is a diffusional component which must also be considered. Central to the development of this hypothesis are the appropriate experimental systems, which can be manipulated using the tools of molecular genetics. Escherichia coli and Saccharomyces cerevisiae are ideally suited as model systems to study this process in that both (i) exhibit saturable long-chain fatty acid transport at low l...

The translation of picornavirus RNA occurs by a cap-independent mechanism directed by a region of about 450 nucleotides from the 5&#39; untranslated region, termed an internal ribosome entry site (IRES). Internal initiation of protein synthesis occurs without any requirement for viral proteins. Furthermore, it is maintained when host cell protein synthesis is almost abolished. By using in vitro translation systems, two distinct families of IRES elements which have very different predicted RNA secondary structures have been defined. The cardiovirus and aphthovirus elements function very efficiently in rabbit reticulocyte lysate, whereas the enterovirus and rhinovirus elements function poorly in this system. However, supplementation of this translation system with additional cellular proteins can stimulate translation directed by the enterovirus and rhinovirus RNAs and reduce production of aberrant initiation products. The characterization of cellular proteins interacting with the pic...

Human T-cell lymphotropic virus type 1 (HTLV-1) infection is associated with a diverse range of lymphoproliferative and neurodegenerative diseases, yet pathogenic mechanisms induced by the virus remain obscure. This complex retrovirus contains typical structural and enzymatic genes but also unique regulatory and accessory genes in four open reading frames (ORFs) of the pX region of the viral genome (pX ORFs I to IV). The regulatory proteins encoded by pX ORFs III and IV, Tax and Rex, respectively, have been extensively characterized. In contrast the contribution of the four accessory proteins p12(I), p27(I), p13(II), and p30(II), encoded by pX ORFs I and II, to viral replication and pathogenesis remained unclear. Proviral clones that are mutated in either pX ORF I or II, while fully competent in cell culture, are severely limited in their replicative capacity in a rabbit model. Emerging evidence indicates that the HTLV-1 accessory proteins are critical for establishment of viral infectivity, enhance T-lymphocyte activation, and potentially alter gene transcription and mitochondrial function. HTLV-1 pX ORF I expression is critical to the viral infectivity in resting primary lymphocytes, suggesting a role for p12(I) in lymphocyte activation. The endoplasmic reticulum and cis-Golgi localizing p12(I), encoded from pX ORF I, activates NFAT, a key T-cell transcription factor, through calcium-mediated signaling pathways and may lower the threshold of lymphocyte activation via the JAK/STAT pathway. In contrast p30(II) localizes to the nucleus and represses viral promoter activity, but may regulate cellular gene expression through p300/CBP or related coactivators of transcription. p13(II) targets mitochondrial proteins, where it alters the organelle morphology and may influence energy metabolism. Collectively, studies of the molecular functions of the HTLV-1 accessory proteins provide insight into strategies used by retroviruses that are associated with lymphoproliferative diseases.

SUMMARY Bacteriophages belonging to the order Caudovirales possess a tail acting as a molecular nanomachine used during infection to recognize the host cell wall, attach to it, pierce it, and ensure the high-efficiency delivery of the genomic DNA to the host cytoplasm. In this review, we provide a comprehensive analysis of the various proteins constituting tailed bacteriophages from a structural viewpoint. To this end, we had in mind to pinpoint the resemblances within and between functional modules such as capsid/tail connectors, the tails themselves, or the tail distal host recognition devices, termed baseplates. This comparison has been extended to bacterial machineries embedded in the cell wall, for which shared molecular homology with phages has been recently revealed. This is the case for the type VI secretion system (T6SS), an inverted phage tail at the bacterial surface, or bacteriocins. Gathering all these data, we propose that a unique ancestral protein fold may have given...

Proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. In bacteria, several targeting routes are known; the SecB- and the signal recognition particle-dependent pathways are the best characterized. Recently, evidence for the existence of a third major route, the twin-Arg pathway, was gathered. Proteins that use either one of these three different pathways possess special features that enable their specific interaction with the components of the targeting routes. Such targeting information is often contained in an N-terminal extension, the signal sequence, but can also be found within the mature domain of the targeted protein. Once the nascent chain starts to emerge from the ribosome, competition for the protein between different targeting factors begins. After recognition and binding, the targeting factor delivers the protein to the translocation sites...

Presentazione dal titolo "Introduzione alla biologia molecolare di Mycoplasma sp." Contenuti: - Biologia molecolare dei micoplasmi - Cenni di epidemiologia - Meccanismo di infezione delle cellule - Principali patologie nell'uomo - Micoplasmi e trasformazione neoplastica - PTI-1 - Relazione tra PTI-1 e infezione da micoplasma [ENG] Presentation entitled "Introduction to the molecular biology of Mycoplasma sp." Contents: - Molecular biology of mycoplasmas - Outlines of epidemiology - Mechanism of cell infection - Main pathologies in humans - Mycoplasms and neoplastic transformation - PTI-1 - Relationship between PTI-1 and mycoplasma infection