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Fulltext Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory

Baharin A, Ting TY, Goh HH

Plants (Basel), 2023 Jan 15;12(2).
PMID: 36679121 DOI: 10.3390/plants12020408

Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
Fulltext Morphine and Phoenix dactylifera (dates) effects on the histological features of male rat reproductive organs

Baharin A, Hashim NE, Sonsudin F, Hashim NH

J Res Med Sci, 2020;25:20.
PMID: 32174992 DOI: 10.4103/jrms.JRMS_681_16

Background: Previous studies have shown that morphine negatively effects male fertility while Phoenix dactylifera (dates) could cure male infertility by the exhibition of antagonist effects. This study was conducted to assess the possible ameliorating effects of dates on the histological features of morphine-induced male rat reproductive organs.
Materials and Methods: Adult male Sprague Dawley rats age 7-9 weeks old, 200-250 g body weight (BW) were divided into six rats per each group: Group 1, force-fed with distilled water, 1 ml/kg BW for 35 days (control); Group 2, intramuscularly (IM) injected with morphine, 20 mg/kg BW for 7 days followed by force-fed with distilled water for 28 days; Group 3, force-fed with distilled water for 7 days followed by crude P. dactylifera extract, 200 mg/kg for 28 days; Group 4, injected (IM) with morphine, 20 mg/kg BW for 7 days followed by force-fed of crude P. dactylifera extract, 200 mg/kg for 28 days. Rats were sacrificed on day 36. The seminal vesicle (SV) and prostate gland (PG) were removed and fixed before histological processes.
Results: In morphine-treated rats, the SV showed the absence of honeycomb-like appearance with flattened columnar cells while in the PG, eosinophilic secretion was noted to be absent from glandular lumina as compared to the control group. Administration of P. dactylifera extract in Group 4 showed improvement in histoarchitecture of the SV and PG with complex mucosal infoldings and glands luminal filled with secretion.
Conclusion: P. dactylifera extract has a protective effect against the adverse effects of morphine on the male rat reproductive organs.
Fulltext Transcriptome-wide shift from photosynthesis and energy metabolism upon endogenous fluid protein depletion in young Nepenthes ampullaria pitchers

Goh HH, Baharin A, Mohd Salleh F', Ravee R, Wan Zakaria WNA, Mohd Noor N

Sci Rep, 2020 04 20;10(1):6575.
PMID: 32313042 DOI: 10.1038/s41598-020-63696-z

Carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. The transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.
The the the the induction of jamais vu in the laboratory: word alienation and semantic satiation

Moulin CJA, Bell N, Turunen M, Baharin A, O'Connor AR

Memory, 2021 Aug;29(7):933-942.
PMID: 32079491 DOI: 10.1080/09658211.2020.1727519

Jamais vu is a phenomenon operationalised as the opposite of déjà vu, i.e. finding subjectively unfamiliar something that we know to be familiar. We sought to document that the subjective experience of jamais vu can be produced in word alienation tasks, hypothesising that déjà vu and jamais vu are similar experiential memory phenomena. Participants repeatedly copied words until they felt "peculiar", had completed the task, or had another reason to stop. About two-thirds of all participants (in about one-third of all trials) reported strange subjective experiences during the task. Participants reported feeling peculiar after about thirty repetitions, or one minute. We describe these experiences as jamais vu. This experimentally induced phenomenon was related to real-world experiences of unfamiliarity. Although we replicated known patterns of correlations with déjà vu (age and dissociative experiences), the same pattern was not found for our experimental analogue of jamais vu, suggesting some differences between the two phenomena. However, in daily life, those people who had déjà vu more frequently also had jamais vu more frequently. Findings are discussed with reference to the progress that has been made in déjà vu research in recent years, with a view to fast-tracking our understanding of jamais vu.
Protease activity is maintained in Nepenthes ampullaria digestive fluids depleted of endogenous proteins with compositional changes

Ravee R, Baharin A, Cho WT, Ting TY, Goh HH

Physiol Plant, 2021 Dec;173(4):1967-1978.
PMID: 34455610 DOI: 10.1111/ppl.13540

Nepenthes ampullaria is a unique carnivorous tropical pitcher plant with the detritivorous capability of sequestering nutrients from leaf litter apart from being insectivorous. The changes in the protein composition and protease activity of its pitcher fluids during the early opening of pitchers (D0 and D3C) were investigated via a proteomics approach and a controlled protein depletion experiment (D3L). A total of 193 proteins were identified. Common proteins such as pathogenesis-related protein, proteases (Nep [EC:3.4.23.12], SCP [EC:3.4.16.-]), peroxidase [EC:1.11.1.7], GDSL esterase/lipase [EC:3.1.1.-], and purple acid phosphatase [EC:3.1.3.2] were found in high abundance in the D0 pitchers and were replenished in D3L samples. This reflects their importance for biological processes upon pitcher opening. Meanwhile, prey-inducible chitinases [EC:3.2.1.14] were found in D0 but not in D3C and D3L samples, which suggests their degradation in the absence of prey. Protease activity assays demonstrated the replenishment of proteases in D3L with similar levels of proteolytic activities to that of D3C samples. This supports a feedback mechanism and signaling in the molecular regulation of endogenous protein secretion, turnover, and activity in Nepenthes pitcher fluids. Furthermore, we also discovered several new enzymes (XTH [EC:2.4.1.207], PAE [EC:3.1.1.98]) with possible functions in cell wall degradation that could contribute to the detritivory habit of N. ampullaria.