Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

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Isolation of a heat-stable maize endosperm ADP-glucose pyrophosphorylase variant

Heat stress reduces maize yield and several lines of evidence suggest that the heat lability of maize endosperm ADP-glucose pyrophosphorylase (AGPase) contributes to this yield loss. AGPase catalyzes a rate-limiting step in starch synthesis. Herein, we present a novel maize endosperm AGPase small subunit variant, termed BT2-TI that harbors a single amino acid change of residue 462 from threonine to isoleucine. The mutant was isolated by random mutagenesis and heterologous expression in a bacterial system. BT2-TI exhibits enhanced heat stability compared to wildtype maize endosperm AGPase.The TI mutation was placed into another heat-stable small subunit variant, MP. MP is composed of sequences from the maize endosperm and the potato tuber small subunit. The MP-TI small subunit variant exhibited greater heat stability than did MP. Characterization of heat stability as well as kinetic and allosteric properties suggests that MP-TI may lead to increased starch yield when expressed in monocot endosperms.     

An “orientation sphere” visualization for examining animal head movements

1. Animal behavior is elicited, in part, in response to external conditions, but understanding how animals perceive the environment and make the decisions that bring about these behavioral responses is challenging.
2. Animal heads often move during specific behaviors and, additionally, typically have sensory systems (notably vision, smell, and hearing) sampling in defined arcs (normally to the front of their heads). As such, head‐mounted electronic sensors consisting of accelerometers and magnetometers, which can be used to determine the movement and directionality of animal heads (where head “movement” is defined here as changes in heading [azimuth] and/or pitch [elevation angle]), can potentially provide information both on behaviors in general and also clarify which parts of the environment the animals might be prioritizing (“environmental framing”).
3. We propose a new approach to visualize the data of such head‐mounted tags that combines the instantaneous outputs of head heading and pitch in a single intuitive spherical plot. This sphere has magnetic heading denoted by “longitude” position and head pitch by “latitude” on this “orientation sphere” (O‐sphere).
4. We construct the O‐sphere for the head rotations of a number of vertebrates with contrasting body shape and ecology (oryx, sheep, tortoises, and turtles), illustrating various behaviors, including foraging, walking, and environmental scanning. We also propose correcting head orientations for body orientations to highlight specific heading‐independent head rotation, and propose the derivation of O‐sphere‐metrics, such as angular speed across the sphere. This should help identify the functions of various head behaviors.
5. Visualizations of the O‐sphere provide an intuitive representation of animal behavior manifest via head orientation and rotation. This has ramifications for quantifying and understanding behaviors ranging from navigation through vigilance to feeding and, when used in tandem with body movement, should provide an important link between perception of the environment and response to it in free‐ranging animals.

     

Chlamydia trachomatis Infection of Endocervical Epithelial Cells Enhances Early HIV Transmission Events

Chlamydia trachomatis causes a predominantly asymptomatic, but generally inflammatory, genital infection that is associated with an increased risk for HIV acquisition. Endocervical epithelial cells provide the major niche for this obligate intracellular bacterium in women, and the endocervix is also a tissue in which HIV transmission can occur. The mechanism by which CT infection enhances HIV susceptibility at this site, however, is not well understood. Utilizing the A2EN immortalized endocervical epithelial cell line grown on cell culture inserts, we evaluated the direct role that CT-infected epithelial cells play in facilitating HIV transmission events. We determined that CT infection significantly enhanced the apical-to-basolateral migration of cell-associated, but not cell-free, HIV_BaL, a CCR5-tropic strain of virus, across the endocervical epithelial barrier. We also established that basolateral supernatants from CT-infected A2EN cells significantly enhanced HIV replication in peripheral mononuclear cells and a CCR5+ T cell line. These results suggest that CT infection of endocervical epithelial cells could facilitate both HIV crossing the mucosal barrier and subsequent infection or replication in underlying target cells. Our studies provide a mechanism by which this common STI could potentially promote the establishment of founder virus populations and the maintenance of local HIV reservoirs in the endocervix. Development of an HIV/STI co-infection model also provides a tool to further explore the role of other sexually transmitted infections in enhancing HIV acquisition.     

Cellulases and xylanase of an anaerobic rumen fungus grown on wheat straw, wheat straw holocellulose, cellulose, and xylan

The activities of cellulolytic and xylanolytic enzymes produced by an anaerobic fungus (R1) which resembled Neocallimastix sp. were investigated. Carboxymethylcellulase (CMCase), cellobiase, and filter paper (FPase) activities had pH optima of 6.0, 5.5, and 6.0, respectively. CMCase and cellobiase activities both had a temperature optimum of 50 degrees C, whereas FPase had an optimum of 45 degrees C. The pH and temperature optima for xylanase activity were pH 6.0 and 50 degrees C, respectively. Growth of the fungus on wheat straw, wheat straw holocellulose, or cellulose resulted in substantial colonization, with at least 43 to 58% losses in substrate dry matter and accumulation of comparable amounts of formate. This end product was correlated to apparent loss of substrate dry weight and could be used as an indicator of fungal growth. Milling of wheat straw did not enhance the rate or extent of substrate degradation. Growth of the R1 isolate on the above substrates or xylan also resulted in accumulation of high levels of xylanase activity and lower cellulase activities. Of the cellulases, CMCase was the most active and was associated with either low or trace amounts of cellobiase and FPase activities. During growth on xylan, reducing sugars, including arabinose and xylose, rapidly accumulated in the medium. Xylose and other reducing sugars, but not arabinose, were subsequently used for growth. Reducing sugars also accumulated, but not as rapidly, when the fungus was grown on wheat straw, wheat straw holocellulose, or cellulose. Xylanase activities detected during growth of R1 on media containing glucose, xylose, or cellobiose suggested that enzyme production was constitutive.(ABSTRACT TRUNCATED AT 250 WORDS)     

Effect of phenolic acids and phenolics from plant cell walls on rumenlike fermentation in consecutive batch culture

Information on the interaction between mixed populations in the rumen and plant phenolics is required to fully elucidate the limitations of phenolic compounds on forage digestibility. The objective of this study was to examine the degradation of Italian ryegrass (Lolium multiflorum L.) hay incubated with mixed ruminal populations in consecutive batch culture (CBC) with or without phenolic acids or phenolic compounds extracted from plant cell walls. Each CBC consisted of a series of 10 cultures (3 replicates per culture) inoculated (10%, vol/vol) in sequence at 48-h intervals with microbial suspension from the previous set of cultures. All cultures were grown on a semidefined medium containing Italian ryegrass hay, and each CBC was initiated with an inoculum from the rumen. Rumenlike fermentation characteristics were maintained in control CBCs by repeated inoculum transfer. Treatment CBCs were transferred as described above, but cultures 5, 6, and 7 were incubated in the presence of trans-p-coumaric, cis-p-coumaric, or trans-ferulic acid or phenolics extracted from the cell walls of maize stem or barley straw. Mean apparent dry matter disappearance in control CBC cultures was 495 mg per g of hay, whereas the presence of phenolics reduced the initial dry matter disappearance by 6.3 to 25.6%. trans-p-Coumaric acid and, to a lesser extent, the phenolics from cell walls of maize stem were the most inhibitory compounds for dry matter disappearance and for the production of volatile fatty acids; trans-p-coumaric acid altered the molar ratio of acetate/propionate/butyrate. The CBC further showed variations in the ability of the rumen microbial population to adapt to phenolic compounds.     

Effect of phenolic acids and phenolics from plant cell walls on rumenlike fermentation in consecutive batch culture.

Information on the interaction between mixed populations in the rumen and plant phenolics is required to fully elucidate the limitations of phenolic compounds on forage digestibility. The objective of this study was to examine the degradation of Italian ryegrass (Lolium multiflorum L.) hay incubated with mixed ruminal populations in consecutive batch culture (CBC) with or without phenolic acids or phenolic compounds extracted from plant cell walls. Each CBC consisted of a series of 10 cultures (3 replicates per culture) inoculated (10%, vol/vol) in sequence at 48-h intervals with microbial suspension from the previous set of cultures. All cultures were grown on a semidefined medium containing Italian ryegrass hay, and each CBC was initiated with an inoculum from the rumen. Rumenlike fermentation characteristics were maintained in control CBCs by repeated inoculum transfer. Treatment CBCs were transferred as described above, but cultures 5, 6, and 7 were incubated in the presence of trans-p-coumaric, cis-p-coumaric, or trans-ferulic acid or phenolics extracted from the cell walls of maize stem or barley straw. Mean apparent dry matter disappearance in control CBC cultures was 495 mg per g of hay, whereas the presence of phenolics reduced the initial dry matter disappearance by 6.3 to 25.6%. trans-p-Coumaric acid and, to a lesser extent, the phenolics from cell walls of maize stem were the most inhibitory compounds for dry matter disappearance and for the production of volatile fatty acids; trans-p-coumaric acid altered the molar ratio of acetate/propionate/butyrate. The CBC further showed variations in the ability of the rumen microbial population to adapt to phenolic compounds.     

Growth and fermentation of an anaerobic rumen fungus on various carbon sources and effect of temperature on development.

An anaerobic fungus (strain R1) resembling Neocallimastix spp. was isolated from sheep rumen. When grown on defined medium, the isolate utilized a wide range of polysaccharides and disaccharides, but of the eight monosaccharides tested only fructose, glucose, and xylose supported growth. The organism had doubling times of 5.56 h on glucose and 6.67 h on xylose, and in each case fermentation resulted in production of formate, acetate, lactate, and ethanol. During active growth, formate was a reliable indicator of fungal biomass. Growth on a medium containing glucose and xylose resulted in a doubling time of 8.70 h, but diauxic growth did not occur since both sugars were utilized simultaneously. The optimum temperature for zoospore and immature plant development was 39 degrees C, and no development occurred below 33 degrees C or above 41 degrees C.     

Techniques in molecular biology

Book Review

Techniques in molecular biologyJ.M. Walker and W. Gaastra (Eds.), vol. 2. London: Croom Helm, 1987. iv + 332 pages. £14.95. ISBN 0-7099-3673-7