HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening

The Swiss Light Source facilitates fragment-based drug-discovery campaigns for academic and industrial users through the Fast Fragment and Compound Screening (FFCS) software suite. This framework is further enriched by the option to utilize the Smart Digital User (SDU) software for automated data collection across the PXI, PXII and PXIII beamlines. In this work, the newly developed HEIDI webpage (https://heidi.psi.ch) is introduced: a platform crafted using state-of-the-art software architecture and web technologies for sample management of rotational data experiments. The HEIDI webpage features a data-review tab for enhanced result visualization and provides programmatic access through a representational state transfer application programming interface (REST API). The migration of the local FFCS MongoDB instance to the cloud is highlighted and detailed. This transition ensures secure, encrypted and consistently accessible data through a robust and reliable REST API tailored for the FFCS software suite. Collectively, these advancements not only significantly elevate the user experience, but also pave the way for future expansions and improvements in the capabilities of the system.

Effect of low-roughage diets on the microflora and lipid metabolism in the rumen

Changing the diet of five lactating cows and one nonlactating cow from high to low roughage induced milk fat depression in the lactating cows and altered the composition of the rumen microflora. While the numbers of lactic and propionic acid-producing bacteria increased, the numbers of Butyrivibrio spp. decreased. The numbers of lipolytic bacteria and the in vitro lipolytic activity of the rumen fluid were also decreased, as was the extent of hydrogenation of linoleic and linolenic acids combined in soybean oil incubated in vitro with rumen fluid. It is suggested that among the bacterial population in the rumen the vibrios, which were adversely affected by the low-roughage diets, may contribute significantly to both lipolysis and hydrogenation in the rumen.

Upheaval in the bacterial nucleoid. An active chromosome segregation mechanism

Recent advances have completely overturned the classical view of chromosome segregation in bacteria. Far from being a passive process involving gradual separation of the chromosomes, an active, possibly mitotic-like machinery is now known to exist. Soon after the initiation of DNA replication, the newly replicated copies of the oriC region, behaving rather like eukaryotic centromeres, move rapidly apart towards opposite poles of the cell. They then determine the positions that will be taken up by the newly formed sister nucleoids when DNA replication has been completed. Thus, the gradual expansion of the diffuse nucleoid camouflages an underlying active mechanism. Several genes involved in chromosome segregation in bacteria have now been defined; their possible functions are discussed.

Polar localization of the MinD protein of Bacillus subtilis and its role in selection of the mid-cell division site

Cell division in rod-shaped bacteria is initiated by formation of a ring of the tubulin-like protein FtsZ at mid-cell. Division site selection is controlled by a conserved division inhibitor MinCD, which prevents aberrant division at the cell poles. The Bacillus subtilis DivIVA protein controls the topological specificity of MinCD action. Here we show that DivIVA is targeted to division sites late in their assembly, after some MinCD-sensitive step requiring FtsZ and other division proteins has been passed. DivIVA then recruits MinD to the division sites preventing another division from taking place near the newly formed cell poles. Sequestration of MinD to the poles also releases the next mid-cell sites for division. Remarkably, this mechanism of DivIVA action is completely different from that of the equivalent protein MinE of Escherichia coli, even though both systems operate via the same division inhibitor MinCD.

A fixed distance for separation of newly replicated copies of oriC in Bacillus subtilis: implications for co-ordination of chromosome segregation and cell division

The Spo0J protein of Bacillus subtilis is required for normal chromosome segregation and forms discrete subcellular assemblies closely associated with the oriC region of the chromosome. Here we show that duplication of Spo0J foci occurs early in the DNA replication cycle and that this requires the initiation of DNA replication at oriC but not elongation beyond the nearby STer sites. Soon after duplication, sister oriC/Spo0J foci move rapidly apart to achieve a fixed separation of about 0.7 microm, reminiscent of the segregation of eukaryotic chromosomes on the mitotic spindle. The magnitude of the fixed separation distance may explain how chromosome segregation is kept in close register with cell growth and the initiation mass for DNA replication. It could also explain how segregation can proceed accurately in the absence of cell division. The kinetics of focal separation suggest that one role of Spo0J protein may be to facilitate formation of separate sister oriC complexes that can be segregated.

Bacillus subtilis cell cycle as studied by fluorescence microscopy: constancy of cell length at initiation of DNA replication and evidence for active nucleoid partitioning

Fluorescence microscopic methods have been used to characterize the cell cycle of Bacillus subtilis at four different growth rates. The data obtained have been used to derive models for cell cycle progression. Like that of Escherichia coli, the period required by B. subtilis for chromosome replication at 37 degrees C was found to be fairly constant (although a little longer, at about 55 min), as was the cell mass at initiation of DNA replication. The cell cycle of B. subtilis differed from that of E. coli in that changes in growth rate affected the average cell length but not the width and also in the relative variability of period between termination of DNA replication and septation. Overall movement of the nucleoid was found to occur smoothly, as in E. coli, but other aspects of nucleoid behavior were consistent with an underlying active partitioning machinery. The models for cell cycle progression in B. subtilis should facilitate the interpretation of data obtained from the recently introduced cytological methods for imaging the assembly and movement of proteins involved in cell cycle dynamics.

Dynamic, mitotic-like behavior of a bacterial protein required for accurate chromosome partitioning

The Bacillus subtilis spo0J gene is required for accurate chromosome partitioning during growth and sporulation. We have characterized the subcellular localization of Spo0J protein by immunofluorescence and, in living cells, by use of a spo0J-gfp fusion. We show that the Spo0J protein forms discrete stable foci usually located close to the cell poles. The foci replicate in concert with the initiation of new rounds of DNA replication, after which the daughter foci migrate apart inside the cell. This migration is independent of cell length extension, and presumably serves to direct the daughter chromosomes toward opposite poles of the cell, ready for division. During sporulation, the foci move to the extreme poles of the cell, where they function to position the oriC region of the chromosome ready for polar septation. These observations provide strong evidence for the existence of a dynamic, mitotic-like apparatus responsible for chromosome partitioning in bacteria.

The Bacillus subtilis soj-spo0J locus is required for a centromere-like function involved in prespore chromosome partitioning

During sporulation in Bacillus subtilis a small prespore cell is formed by an asymmetric cell division. Pre-spore chromosome partitioning occurs by a specialised mechanism in which septation precedes chromosome movement. We show that the spo0J gene is needed to specify the orientation of the chromosome at the time of polar division and to impose directionality on the subsequent transport of the remainder of the chromosome through the septum. Both phenotypes may arise by disruption of a centromere-like apparatus that anchors the or/C region of the prespore chromosome in the pole of the cell.

Postseptational chromosome partitioning in bacteria

Mutations in the spoIIIE gene prevent proper partitioning of one chromosome into the developing prespore during sporulation but have no overt effect on partitioning in vegetatively dividing cells. However, the expression of spoIIIE in vegetative cells and the occurrence of genes closely related to spoIIIE in a range of nonsporulating eubacteria suggested a more general function for the protein. Here we show that SpoIIIE protein is needed for optimal chromosome partitioning in vegetative cells of Bacillus subtilis when the normal tight coordination between septation and nucleoid partitioning is perturbed or when septum positioning is altered. A functional SpoIIIE protein allows cells to recover from a state in which their chromosome has been trapped by a closing septum. By analogy to its function during sporulation, we suggest that SpoIIIE facilitates partitioning by actively translocating the chromosome out of the septum. In addition to enhancing the fidelity of nucleoid partitioning, SpoIIIE also seems to be required for maximal resistance to antibiotics that interfere with DNA metabolism. The results have important implications for our understanding of the functions of genes involved in the primary partitioning machinery in bacteria and of how septum placement is controlled.

Glycerol teichoic acid as an antigenic determinant in a Gram-negative bacterium Butyrivibrio fibrisolvens

An antigenic determinant isolated from a strain of the Gram-negative bacterium Butyrivibrio fibrisolvens reacted with specific antisera to the polyglycerophosphate backbone of membrane teichoic acids of lactobacilli. It gave a reaction of identity with membrane glycerol lipoteichoic acid and glycerol teichoic acid preparations from lactobacilli, and with phenol extracts of other Gram-positive bacteria. The antigen-antibody reactions was strongly inhibited by glycerol-phosphoryl-glycerol-phosphoryl-glycerol and the chemical composition was consistent with glycerol teichoic acid. It was concluded that this Gram-negative bacterium contained a glycerol teichoic acid whose polyglycerophospate backbone was acting as antigenic determinant. Extracts of 33 out of 52 other strains of butyrivibrios examined gave similar reactions.

Characterization of two strains of cariogenic lactobacilli

Two strains of lactobacilli that initiate dental caries in conventional animals were exained for their physiological and serological characteristics. The strain designated V CL-25 was identified as Lactobacillus fermentum and belonged to serological group F. The strain designated IV CL-37 was a Lactobacillus salivarius, but it could not be further identified as either of the known subspecies, nor did it belong to serological group G.

Isolation of lipoteichoic acids from Butyrivibrio fibrisolvens

Lipoteichoic acid (LTA) and deacylated lipoteichoic acid have been isolated from the bovine-rumen Gram-negative anaerobe Butyrivibrio fibrisolvens by phenol extraction. Lipoteichoic acid (21.8 mumol phosphorus/g cells) consisted of a conventional 1, 3-phosphodiester-linked chain of glycerol phosphate units joined covalently to a glycolipid. It was not substituted with glycosyl or D-alalyl ester groups. Deacylated lipoteichoic acid (57.5 mumol phosphorus/g cells) was similar in constitution but lacked fatty acid esters. Lipoteichoic acid reacted serologically with antisera to the glycerol phosphate backbone of known lipoteichoic acids. The presence of similar teichoic acid polymers has also been demonstrated in some other strains of B. fibrisolvens and this is of significance in demonstrating that teichoic acids can occur in Gram-negative bacteria.

Common antigenic determinant in a rumen organism and in salmonellae containing the antigen O4

Nineteen of 28 strains of rumen organisms isolated from a cow on a high roughage diet and identified morphologically as butyrivibrios, reacted to a low agglutinin titer with salmonella antisera, forming five groups. However only one strain reacted with polyvalent O salmonella antiserum. This strain reacted with O4 factor serum and with antisera to Salmonella strains containing the antigen O4, and agglutinin absorption tests showed the presence of an antigen identical to O4. When 16 further strains of butyrivibrio-like rumen organisms isolated from three cows and one steer were examined, one possessed an antigen similar to but not identical with the antigen O9, and two strains reacted with specific O6,7 factor serum but were not examined further. These four strains were presumptively identified by physiological tests as butyrivibrios. The possible site of antigenic stimulation by such organisms is discussed.

Some slime-forming heterofermentative species of the genus Lactobacillus

Lactobacillus coprophilus subsp. confusus (NCDO 1586) and 18 other strains of slime-forming heterofermentative lactobacilli obtained from diverse sources are considered to form a new species on the basis of their physiological characteristics and similarities of their pyruvate reductases and lactate dehydrogenases. It is suggested that these strains should be named Lactobacillus confusus (Holzapfel & Kandler) comb. nov. (L. coprophilus subsp. confusus Holzapfel & Kandler), reasons being given. The type strain is NCDO 1586 (NCIB 9311, ATCC 10881). Strains of Lactobacillus vermiforme and Lactobacillus viridescens also form slime. However, L. vermiforme was readily separated from the other two by the criteria used. Although physiological characteristics separated L. viridescens from L. confusus, a relationship between these two species and also between them and the leuconostocs was indicated by the properties of the pyruvate reductases and lactate dehydrogenases. The slime produced by all species was found to be a glucan, probably a dextran, containing primarily alpha-1-6-glycosidic linkages.