Biology subjects

de los Reyes, B. G.

Publications and source records attributed to de los Reyes, B. G..

4 recordsLinked to original sources

bioRxiv2021

Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation

Because of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are needed. This study evaluated the dose x time effects on the anti-microbial action of ozone (O3) gas against the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, which are common contaminants in fresh produce. The study on non-host tomato environment correlated the dose x time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 g O3/g of fruit) and moderate (2 g O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 g/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components. Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.

microbiology↗

bioRxiv2021

Yield Maintenance Under Drought is Orchestrated by the qDTY12.1-Encoded DECUSSATE Gene of Rice Through a Network With Other Flowering-Associated Genes Across the Genetic Background

Introgression of major-effect QTLs is an important component of rice breeding for yield-retention under drought. While largely effective, the maximum potentials of such QTLs have not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background could either enhance or undermine the QTL effects. To elucidate the molecular underpinnings of such interaction, we dissected qDTY12.1 synergy with numerous peripheral genes in context of network rewiring effects. By integrative transcriptome profiling and network modeling, we identified the DECUSSATE (OsDEC) within qDTY12.1 as the core of the synergy and shared by two sibling introgression lines in IR64 genetic background, i.e., LPB (low-yield penalty) and HPB (high-yield penalty). OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway, which are lacking in HPB. Results further support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. We propose that the functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the depletion of photosyntate needed for reproductive growth due to drought. Its impact on yield-retention is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought. Author summaryWhile the Green Revolution of the 1960s significantly increased rice grain yields through the creation of high-yielding varieties for high input systems, current marginal climates pose a significant challenge for providing consistent yield. In rice growing regions of the world, drought affects the livelihood of small-scale and subsistence farmers by inflicting significant yield penalties to their production systems. Breeding of next-generation rice varieties with optimal balance of survivability and productivity traits will be key to providing consistent yields year to year. Within this paradigm, the use of large effect QTLs such as qDTY12.1 to improve yield retention under drought have been largely successful. By integrating the use of high resolution transcriptome datasets with a focused biological interrogation of agronomic results from this and previous studies, we uncovered a putative functional genetic network, anchored by the DECUSSATE gene (OsDEC) within qDTY12.1, that effectively minimizes drought penalties to yield by driving cellular processes that culminate in timely flowering that maximizes the use of photosynthetic sources for efficient reproduductive transition and ultimately seed development. Our study further illuminates the qDTY12.1 function and speaks to the misconception that qDTY introgression alone is sufficient for providing consistently large positive effects to yield retention under reproductive stage drought.

genetics↗

bioRxiv2020

Transgressive segregation for salt tolerance in rice due to physiological coupling and uncoupling and genetic network rewiring

Transgressive segregation is common in plant breeding populations, where a small minority of recombinants are outliers relative to parental phenotypes. While this phenomenon has been attributed to complementation and epistatic effects, the physiological, biochemical, and molecular bases have not been fully illuminated. By systems-level scrutiny of the IR29 x Pokkali recombinant inbred population of rice, we addressed the hypothesis that novel salt tolerance phenotypes are created by positive or negative coupling or uncoupling effects and novel regulatory networks. Hyperspectral profiling distinguished the transgressive individuals in terms of stress penalty to growth. Non-parental network signatures that led to either optimal or non-optimal integration of developmental with stress-related mechanisms were evident at the macro-physiological, biochemical, metabolic, and transcriptomic levels. The large positive net gain in super-tolerant progeny was due to ideal complementation of beneficial traits, while shedding antagonistic traits. Super-sensitivity was explained by the stacking of multiple antagonistic traits and loss of major beneficial traits. The mechanisms elucidated in this study are consistent with the Omnigenic Theory, emphasizing the synergy or lack thereof between core and peripheral components. This study supports a breeding paradigm based on genomic modeling to create the novel adaptive phenotypes for the crops of the 21st century.

genetics↗

bioRxiv2019

Physiological networks governing salinity tolerance potentials in Gossypium hirsutum germplasm

Toxic ions begin to accumulate in tissues of salt-stressed plants after the initial osmotic shock. In glycophytes, the ability to mobilize or sequester excess ions define tolerance mechanisms. Mobilization and sequestration of excess Na+ involves three transport mechanisms facilitated by the plasma membrane H+/Na+ antiporter (SOS1), vacuolar H+/Na+ antiporter (NHX1), and Na+/K+ transporter in vascular tissues (HKT1). While the cultivated Gossypium hirsutum (upland cotton) is significantly more tolerant to salinity relative to other crops, the critical factors contributing to the observed variation for tolerance potential across the germplasm has not been fully scrutinized. In this study, the spatio-temporal patterns of Na+ accumulation at different severities of salt stress were investigated across a minimal comparative panel representing the spectrum of genetic diversity across the improved cotton germplasm. The goal was to define the importance of integrative or network effects relative to the direct effects of Na+ homeostasis mechanisms mediated by GhHKT1, GhSOS1, and GhNHX1. Multi-dimensional physio-morphometric attributes were investigated in univariate and multivariate statistical contexts, as well as the relationship between variables using structural equation modeling. Results showed that mobilized or sequestered Na+ may contribute to the baseline salinity tolerance, but the observed variance in overall tolerance potential across a meaningful subset of the germplasm were more significantly associated to antioxidant capacity, maintenance of stomatal conductance, chlorophyll content, and divalent cations, and other physiological interactions occurring through complex networks. One-Sentence SummaryVariation in salinity tolerance potential across the tetraploid cultivated Gossypium germplasm is better explained by complex physiological networks rather than just cellular Na+ homeostasis.

physiology↗