Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor

New findings on SNP variants of human protein L-isoaspartyl methyltransferase that affect catalytic activity, thermal stability, and aggregation.

Protein L-isoaspartyl methyltransferase (PIMT/PCMT1), a product of the pcmt1 gene, catalyzes repair of abnormal L-isoaspartyl linkages in age-damaged proteins. Pcmt1 knockout mice exhibit a profound neuropathology and die 30-60 days postnatal from an epileptic seizure. Here we characterize four new SNP variants of human PIMT with respect to enzymatic activity, thermal stability, and propensity to aggregation. Under standard assay conditions, L191S, A150V, P174H and A65V showed activity losses of 72%, 64%, 61%, and 11% respectively. By differential scanning fluorimetry, melting temperature deviations were -5.2, -4.5, +0.5, and -3.4°C. SDS-PAGE of purified protein reveal significant aggregation of L191S, A150V, and P174H, but not A65V. We also report new data on three unusual PIMT variants among the 13 recently characterized by our laboratory. A7P and I58V were previously found to have 1.8-2.0 times the activity of WT PIMT in the standard assay; however, upon kinetic analysis, we find both variants exhibit reduced catalytic efficiency (Vmax/Km) due to weak isoaspartyl substrate binding. The near complete loss of activity (<1%) seen in R36C was investigated by comparing activity of two artificial variants. R36K shows 4.6X the activity of R36C, while R36A shows no improvement, suggesting the guanidino nitrogens of the R36 play a key role in binding the methyl donor S-adenosyl-L-methionine (AdoMet). The new findings reported here extend the list of human PIMT variants that may contribute to neurological diseases in the young and the decline of CNS function in the aged

Évaluation de l’impact à long terme de boues STEP sur les microorganismes du sol : zoom sur l’abondance et l’activité de la communauté microbienne dégradant l’atrazine

Communication orale, résuméLes plans d’épandage permettent de valoriser les boues STEP comme source de matières organiques pour amender des sols agricoles. Le bénéfice apporté par l’apport des boues STEP est mitigé par l’apport d’éléments traces métalliques et HAPs les contaminants et dont l’impact sur la qualité des sols restent difficile à évaluer. Dans ce contexte, à la demande de l’ADEME, le Laboratoire Sol et Environnement (LSE, INRA, ENSAIA, Nancy) a mis en place un essai longue-durée sur le site de la Bouzule pour tester à long terme l’apport de boues STEP sur la qualité des sols agricoles. Parmi, les fonctions ciblées, la fonction filtre, responsable de la biodégradation d’intrants chimiques, a été retenue pour évaluer l’impact de boues STEP. Les parcelles de la Bouzule ayant été fréquemment cultivées avec du maïs et en conséquence traités avec l’herbicide atrazine, présentent une microflore capable de minéraliser cet herbicide. L’impact des boues sur la communauté microbienne dégradant l’atrazine a été évalué en mesurant la structure, l’abondance, et l’activité des populations microbiennes dégradant l’atrazine ont été mesurées pour évaluer 10 ans après le dernier épandage de boues STEP, la résilience éventuelle de l’impact causé. Les résultats de cette étude seront présentés

PQS Produced by the Pseudomonas aeruginosa Stress Response Repels Swarms Away from Bacteriophage and Antibiotics.

We investigate the effect of bacteriophage infection and antibiotic treatment on the coordination of swarming, a collective form of flagellum- and pilus-mediated motility in bacteria. We show that phage infection of the opportunistic bacterial pathogen Pseudomonas aeruginosa abolishes swarming motility in the infected subpopulation and induces the release of the Pseudomonas quinolone signaling molecule PQS, which repulses uninfected subpopulations from approaching the infected area. These mechanisms have the overall effect of limiting the infection to a subpopulation, which promotes the survival of the overall population. Antibiotic treatment of P. aeruginosa elicits the same response, abolishing swarming motility and repulsing approaching swarms away from the antibiotic-treated area through a PQS-dependent mechanism. Swarms are entirely repelled from the zone of antibiotic-treated P. aeruginosa, consistent with a form of antibiotic evasion, and are not repelled by antibiotics alone. PQS has multiple functions, including serving as a quorum-sensing molecule, activating an oxidative stress response, and regulating the release of virulence and host-modifying factors. We show that PQS serves additionally as a stress warning signal that causes the greater population to physically avoid cell stress. The stress response at the collective level observed here in P. aeruginosa is consistent with a mechanism that promotes the survival of bacterial populations.IMPORTANCE We uncover a phage- and antibiotic-induced stress response in the clinically important opportunistic pathogen Pseudomonas aeruginosa Phage-infected P. aeruginosa subpopulations are isolated from uninfected subpopulations by the production of a stress-induced signal. Activation of the stress response by antibiotics causes P. aeruginosa to physically be repelled from the area containing antibiotics altogether, consistent with a mechanism of antibiotic evasion. The stress response observed here could increase P. aeruginosa resilience against antibiotic treatment and phage therapy in health care settings, as well as provide a simple evolutionary strategy to avoid areas containing stress

Taxonomic and functional characterization of microbial communities in Technosols constructed for remediation of a contaminated industrial wasteland

International audienceThe construction of Technosols is an emergent technology based on the assemblage of technogenic materials for ecological reclamation of polluted land and waste recycling. Although this technology is in expansion, knowledge about the microbial communities in Technosols is limited, despite their central role in ecosystem functioning. In this 2-year study, the diversity and the abundance of total and functional microbial communities were characterized in two types of Technosols constructed to reclaim contaminated sites. The structure of the microbial community was analyzed by automated ribosomal intergenic spacer analysis fingerprinting in both types of Technosols, and the taxonomic diversity was further assessed by 16S rRNA clone library sequencing. Real-time PCR was used to quantify the abundance of the total bacterial and crenarchaeal community and of the functional guilds involved in N-cycling. 16S rRNA sequencing showed that Proteobacteria was the main phylum in the Technosols (50-80 %). The other significant phyla identified were Bacteroidetes, Firmicutes, Choloroflexi, and Actinobacteria. Real-time PCR quantification of the abundance of ammonia oxidizers, nitrate reducing, and denitrifying microbial communities involved in nitrogen cycling revealed that bacterial ammonia oxidizers were more abundant than crenarchaeal ammonia oxidizers. A high spatial variability of the microbial community, which decreased with time, was also observed. At the phyla and class levels, the composition of the microbial community in constructed Technosols was similar to "natural" soils. Both the total bacteria and microbial guilds involved in N-cycling were abundant, but in contrast to most natural soils, bacteria and not crenarchaea were the numerically dominant ammonia oxidizers in both types of Technosols. The decrease with time of the variability in microbial community structure support early pedogenic evolution of recently constructed Technosols

Polymorphic Variants of Human Protein l-Isoaspartyl Methyltransferase Affect Catalytic Activity, Aggregation, and Thermal Stability

The Rules and Regulations of the Faculty spans the Institute Archives and Special Collections copies of the publication from 1879-2007. They establish the roles and responsibilities of the Standing Committees of the MIT Faculty, governs its legislative processes, and states its regulations pertaining to the academic calendar, admissions, registration, grades, degrees, and more. The Rules and Regulations of the Faculty also describe the processes via which they can be changed by vote of the Faculty. Parts also address important topics related to syllabi, midterms, scheduling assignments at the end of the semester, and final exams. Rules of the Faculty was first published in October 1879. The title was changed to Rules and Regulations of the Faculty in 1937. Current Rules and Regulations can be found here: https://facultygovernance.mit.edu/rules-and-regulation

Polymorphic Variants of Human Protein l-Isoaspartyl Methyltransferase Affect Catalytic Activity, Aggregation, and Thermal Stability

Protein l-isoaspartyl methyltransferase (PIMT/PCMT1), a product of the human pcmt1 gene, catalyzes repair of abnormal l-isoaspartyl linkages in age-damaged proteins. Pcmt1 knock-out mice exhibit a profound neuropathology and die 30-60 days postnatal from an epileptic seizure. Here we express 15 reported variants of human PIMT and characterize them with regard to their enzymatic activity, thermal stability, and propensity to aggregation. One mutation, R36C, renders PIMT completely inactive, whereas two others, A7P and I58V, exhibit activity that is 80-100% higher than wild type. G175R is highly prone to aggregation and has greatly reduced activity. R17S and R17H show markedly enhanced sensitivity to thermal denaturation. Based on previous studies of moderate PIMT variation in humans and mice, we predict that heterozygosity for R36C, G175R, R17S, and R17H will prove detrimental to cognitive function and successful aging, whereas homozygosity (if it ever occurs) will lead to severe neurological problems in the young