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Open Access Publications from the University of California

Scholarly Works (28 results)

  • Article
LBL Publications (2010)

Some 26,000 samples of extremophilic microorganisms grown at LBNL underwent primary screening. Samples showing biological activities of interest were re-grown and secondary screened. Promising novel leads were reverse-engineered and the microbial sequences responsible the relevant biological activity were transferred into major crop plants, such as corn and soybean. Following greenhouse validation, the transgenic plants, which express their own antifungal polypeptides are growing in the field. After completion of the project, DuPont decided to fund three more years of collaborative R&D at LBNL.

    Cover page: Microbially derived crop protection products
    • Article
    • Peer Reviewed
    LBL Publications (2003)

    Bacterial endospore disruption and nucleic acid extraction resulting in DNA of PCR-amplifiable quality and quantity are not trivial. Responding to the needs of the Hazardous Materials Response Unit (HMRU), Laboratory Division, Federal Bureau of Investigation, protocols were developed to close these gaps. Effectiveness and reproducibility of the techniques were validated with laboratory grown pure spores of Bacillus anthracis and its close phylogenetic neighbors, and with spiked soils and damaged samples.

      Cover page: Extraction of PCR-amplifiable genomic DNA from Bacillus anthracis spores
      • Article
      LBL Publications (2013)
      Meeting the needs of agricultural producers requires the continued development of improved transgenic crop protection products. The completed project focused on developing novel enabling technologies of gene discovery and plant transformation to facilitate the generation of such products.
        Cover page: Novel enabling technologies of gene isolation and plant transformation for improved crop protection
        • Article
        LBL Publications (2003)
        The important role of the normal anaerobic intestinal microbiota has been elucidated in humans and some domesticated animals; however, the presence of intestinal anaerobes, let alone their importance in invertebrates are largely unknown. The purpose of this research was to isolate and to identify obligate anaerobic members of the intestinal microbiota of the Pacific white shrimp, Litopenaeus vannamei. Intestinal samples for microbial isolation were taken from shrimp maintained at three salinities (3, 11, 31 ppt) and on a diet containing different protein concentrations. Members of the anaerobic intestinal microbiota were successfully isolated and cultivated in a Bactron II anaerobe chamber. Many of these isolates could not be identified using available biochemical and molecular-level techniques and databases, and consequently, may represent new, yet undescribed taxa. Of the isolates identified, the majority belonged to the genus Clostridium. Strains of the species, C. subterminale and C, beijerinckii were delineated by biochemical tests, while two species, C. butyricum GC subgroup A and C. bifermentans GC subgroup A were identified by whole-cell fatty acid methyl ester analysis. Isolates were tested for the expression of constitutive enzymes using the APIZYM system. The anaerobic bacteria demonstrated enzyme activities of acid and alkaline phosphatases, C4 and C8 esterases, C14 lipases, arylamidases, and glycosidases. Enzyme activities differed with isolates. Generally, strains identified as C. butyricum expressed enzymes for the breakdown of carbohydrates, while strains identified as C. bifermentans produced enzymes for the breakdown of proteins. Most isolates formed phosphatases possibly used for absorption of nutrients.
          Cover page: Possible role of intestinal obligate anaerobic bacteria in the digestive process of pacific white shrimp litopenaeus vannamei
          • Article
          LBL Publications (2000)

          Lake Baikal in Russia, the world's oldest and deepest continental lake lies in south central Siberia, near the border to Mongolia. The lake is 1,643 m deep and has an area of about 46,000 km2. It holds one-fifth of all the terrestrial fresh water on Earth. Lake Baikal occupies the deepest portion of the Baikal Rift Zone. It was formed some 30-45 million years ago. The isolated Lake Baikal ecosystem represents a unique niche in nature based on its historical formation. The microbial diversity present in this environment has not yet been fully harvested or examined for products and processes of commercial interest and value. Thus, the collection of water, soil, and sub-bottom sediment samples was decided to characterize the microbial diversity of the isolated strains and to screen the isolates for their biotechnological value.

            Cover page: Search for ancient microorganisms in Lake Baikal
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2010)
            Novel dissimilatory perchlorate-reducing bacteria (DPRB) were isolated from enrichments conducted under conditions different from those of all previously described DPRB. Strain LT-1(T) was enriched using medium buffered at pH 6.6 with 2-(N-morpholino)ethanesulfonic acid (MES) and had only 95% 16S rRNA gene identity with its closest relative, Azonexus caeni. Strain MP(T) was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (BER) and together with an additional strain, CR (99% 16S rRNA gene identity), had 97% 16S rRNA gene identity with Propionivibrio limicola. The use of perchlorate and other electron acceptors distinguished strains MP(T) and CR from P. limicola physiologically. Strain LT-1(T) had differences in electron donor utilization and optimum growth temperatures from A. caeni. Strains LT-1(T) and MP(T) are the first DPRB to be described in the Betaproteobacteria outside of the Dechloromonas and Azospira genera. On the basis of phylogenetic and physiological features, strain LT-1(T) represents a novel genus in the Rhodocyclaceae; strain MP(T) represents a novel species within the genus Propionivibrio. The names Dechlorobacter hydrogenophilus gen. nov., sp. nov and Propionivibrio militaris sp. nov. are proposed.
              Cover page: Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov.Creative Commons 'BY-NC' version 4.0 license
              • Article
              • Peer Reviewed
              Climate & Ecosystems (2023)

              Background

              It is known that the gut microbiome of a healthy person affects the process of COVID-19 after getting infected with SARS-CoV-2 virus. It is also believed that colchicine can alleviate the severity of COVID-19.

              Objective

              Current investigations aimed to evaluate the associations between the baseline gut microbiota composition of healthy and Familial Mediterranean fever (FMF) - carrier Armenian men populations, and the severity of the COVID-19 disease after their infection with the SARS-CoV-2. The study has a purpose of answering three core questions: i. Do the characteristics of gut microbiome of Armenians affect the course of COVID-19 severity? ii. How does the COVID-19 disease course on go for FMF patients who have been taking colchicine as a medication over the years after getting infected with SARS-CoV-2? iii. Is there an initial gut micribiota structure pattern for non-FMF and FMF patients in the cases when COVID-19 appears in mild form?

              Methods

              The gut microbiota composition in non-FMF and FMF patients before the first infection (mild and moderate course of COVID-19) was considered. COVID-19 was diagnosed by SARS-CoV-2 nucleic acid RT-PCR in nasopharyngeal swab and/or sputum.

              Results

              The number of patients with male FMF with mild COVID-19 was approximately two times higher than that of non-FMF male subjects with COVID-19. In addition, an association of COVID-19 disease severity with the baseline gut Prevotella, Clostridium hiranonis, Eubacterium biforme, Veillonellaceae, Coprococcus, and Blautia diversities in the non-FMF and FMF populations were revealed by us, which can be used as risk/prognostic factor for the severity of COVID-19.
                Cover page: Host genetics and gut microbiota composition: Baseline gut microbiota composition as a possible prognostic factor for the severity of COVID-19 in patients with familial Mediterranean fever disease
                • Article
                • Peer Reviewed
                LBL Publications (2017)
                The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.
                  Cover page: Draft Genome Sequences of Several Fungal Strains Selected for Exposure to Microgravity at the International Space Station
                  • Article
                  • Peer Reviewed
                  Climate & Ecosystems (2021)
                  Fungi produce secondary metabolites that are not directly involved in their growth, but often contribute to their adaptation to extreme environmental stimuli and enable their survival. Conidial pigment or melanin is one of the secondary metabolites produced naturally by a polyketide synthesis (PKS) gene cluster in several filamentous fungi and is known to protect these fungi from extreme radiation conditions. Several pigmented or melanized fungi have been shown to grow under extreme radiation conditions at the Chernobyl nuclear accident site. Some of these fungi, including Paecilomyces variotii, were observed to grow towards the source of radiation. Therefore, in this study, we wanted to identify if the pigment produced by P. variotii, contributes to providing protection against radiation condition. We first identified the PKS gene responsible for synthesis of pigment in P. variotii and confirmed its role in providing protection against UV irradiation through CRISPR-Cas9 mediated gene deletion. This is the first report that describes the use of CRISPR methodology to create gene deletions in P. variotii. Further, we showed that the pigment produced by this fungus, was not inhibited by DHN-melanin pathway inhibitors, indicating that the fungus does not produce melanin. We then identified the pigment synthesized by the PKS gene of P. variotii, as a naptho-pyrone Ywa1, by heterologously expressing the gene in Aspergillus nidulans. The results obtained will further aid in understanding the mechanistic basis of radiation resistance.
                    Cover page: Identification of the pigment and its role in UV resistance in Paecilomyces variotii, a Chernobyl isolate, using genetic manipulation strategies
                    • Article
                    • Peer Reviewed
                    LBL Publications (2018)
                    Intestinal microorganisms play a crucial role in health and disease. The disruption of host-microbiota homeostasis has been reported to occur not only during disease development but also as a result of medication. Familial Mediterranean fever (FMF) is an inflammatory genetic disease characterized by elevated systemic reactivity against the commensal gut microbiota and high levels of Candida albicans in the gut. This study's major objective was to investigate the effects of commercial probiotic Narine on the relative abundance of gut bacteria (specifically, enterobacteria, lactobacilli, Staphylococcus aureus, and enterococci) of C. albicans carrier and non-carrier FMF patients in remission. Our main finding indicates that the probiotic reduces numbers of C. albicans and abundance of enterobacteria in male and female patients of C. albicans carriers and non-carriers. It has pivotal effect on Enterococcus faecalis: increase in male non-carriers and decrease in female ones regardless of C. albicans status. No effect was seen for Lactobacillus and S. aureus. Our data suggest that M694V/V726A pyrin inflammasome mutations leading to FMF disease may contribute to gender-specific differences in microbial community structure in FMF patients. The study's secondary objective was to elucidate the gender-specific differences in the gut's microbial community of FMF patients. The tendency was detected for higher counts of enterobacteria in female FMF subjects. However, the small number of patients of these groups preclude from conclusive statements, pointing at the need for additional investigations with appropriate for statistical analysis groups of subjects involved in the study.
                      Cover page: Probiotic Lactobacillus acidophilus Strain INMIA 9602 Er 317/402 Administration Reduces the Numbers of Candida albicans and Abundance of Enterobacteria in the Gut Microbiota of Familial Mediterranean Fever Patients
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