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"You, Cai"
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Integrating artificial intelligence in biodiversity conservation: bridging classical and modern approaches
by
Xiong, You-Cai
,
Saqib, Saddam
,
Ullah, Fazal
in
Artificial intelligence
,
Biodiversity
,
biodiversity conservation
2025
Preserving biodiversity is crucial for maintaining ecological balance; however, traditional conservation methods often face various limitations. In most cases, the efficacy of these approaches is frequently constrained by difficulties in scaling and the absence of up-to-date data, hence requiring the incorporation of novel technology. The latest progress in the field of artificial intelligence (AI) offer transformative potential for enhancing contemporary conservation endeavors. There is a growing utilization of AI technologies, like machine learning and data analytics, to improve species identification, habitat monitoring, and threat assessment with exceptional precision and effectiveness. This study explores how AI is incorporated to enhance conventional conservation methods, particularly in the areas such as data analysis, species identification, and habitat monitoring. This paper examines a number of case studies that demonstrate the successful use of AI, with a particular focus on notable advancements in data management, predictive modeling, and resource allocation. The findings highlighted the significance of synergistic methodology that integrates the strength of traditional techniques with the flexibility of contemporary technologies, hence facilitating the development of more resilient conservation solutions. This study also discusses the potential implications for future research and the practical use of AI in the field of conservation. It highlights the strategy of seamless integration to justify both scientific investigation and conservation results.
Journal Article
Novel insights into the interplay between m6A modification and noncoding RNAs in cancer
by
Zhu, Jin-Shui
,
Zhang, Jing
,
Chen, Xiao-Yu
in
Angiogenesis
,
Biomedical and Life Sciences
,
Biomedicine
2020
N6-methyladenosine (m
6
A) is one of the most common RNA modifications in eukaryotes, mainly in messenger RNA (mRNA). Increasing evidence shows that m
6
A methylation modification acts an essential role in various physiological and pathological bioprocesses. Noncoding RNAs (ncRNAs), including miRNAs, lncRNAs and circRNAs, are known to participate in regulating cell differentiation, angiogenesis, immune response, inflammatory response and carcinogenesis. m
6
A regulators, such as METTL3, ALKBH5 and IGF2BP1 have been reported to execute a m
6
A-dependent modification of ncRNAs involved in carcinogenesis. Meanwhile, ncRNAs can target or modulate m
6
A regulators to influence cancer development. In this review, we provide an insight into the interplay between m
6
A modification and ncRNAs in cancer.
Journal Article
Physiological and biochemical responses of soybean plants inoculated with Arbuscular mycorrhizal fungi and Bradyrhizobium under drought stress
by
Sharma, Anket
,
Xiong, You-Cai
,
Farooq, Muhammad
in
Agricultural ecosystems
,
Agriculture
,
Arbuscular mycorrhizas
2021
Background
The present study aims to study the effects of biofertilizers potential of Arbuscular Mycorrhizal Fungi (AMF) and
Bradyrhizobium japonicum
(
B. japonicum
) strains on yield and growth of drought stressed soybean (Giza 111) plants at early pod stage (50 days from sowing, R3) and seed development stage (90 days from sowing, R5).
Results
Highest plant biomass, leaf chlorophyll content, nodulation, and grain yield were observed in the unstressed plants as compared with water stressed-plants at R3 and R5 stages. At soil rhizosphere level, AMF and
B. japonicum
treatments improved bacterial counts and the activities of the enzymes (dehydrogenase and phosphatase) under well-watered and drought stress conditions. Irrespective of the drought effects, AMF and
B. japonicum
treatments improved the growth and yield of soybean under both drought (restrained irrigation) and adequately-watered conditions as compared with untreated plants. The current study revealed that AMF and
B. japonicum
improved catalase (CAT) and peroxidase (POD) in the seeds, and a reverse trend was observed in case of malonaldehyde (MDA) and proline under drought stress. The relative expression of the
CAT
and
POD
genes was up-regulated by the application of biofertilizers treatments under drought stress condition. Interestingly a reverse trend was observed in the case of the relative expression of the genes involved in the proline metabolism such as
P5CS
,
P5CR
,
PDH,
and
P5CDH
under the same conditions. The present study suggests that biofertilizers diminished the inhibitory effect of drought stress on cell development and resulted in a shorter time for DNA accumulation and the cycle of cell division. There were notable changes in the activities of enzymes involved in the secondary metabolism and expression levels of
GmSPS1
,
GmSuSy,
and
GmC-INV
in the plants treated with biofertilizers and exposed to the drought stress at both R3 and R5 stages. These changes in the activities of secondary metabolism and their transcriptional levels caused by biofertilizers may contribute to increasing soybean tolerance to drought stress.
Conclusions
The results of this study suggest that application of biofertilizers to soybean plants is a promising approach to alleviate drought stress effects on growth performance of soybean plants. The integrated application of biofertilizers may help to obtain improved resilience of the agro ecosystems to adverse impacts of climate change and help to improve soil fertility and plant growth under drought stress.
Journal Article
METTL14-mediated m6A modification of circORC5 suppresses gastric cancer progression by regulating miR-30c-2-3p/AKT1S1 axis
by
Chen, Zhao-Yu
,
Chen, Ming
,
Zhang, Jing
in
Antibodies
,
Biomedical and Life Sciences
,
Biomedicine
2022
Background
N6-methyladenosine (m
6
A) RNA methylation and circular RNAs (circRNAs) have been shown to act vital roles in multiple malignancies including gastric cancer (GC). However, there is little knowledge about how m
6
A modification of circRNAs contributes to GC progression.
Methods
The association of METTL14 expression with the clinicopathological characteristics and prognosis in patients with GC was assessed by Western blot, Immunohistochemistry and public datasets. In vitro and vivo function experiments were conducted to investigate the role of METTL14 in GC. Furthermore, m
6
A-circRNA epitranscriptomic microarray was utilized to identify METTL14-mediated m
6
A modification of circRNAs, which were validated by methylated RNA immunoprecipitation (Me-RIP), RT-qPCR and rescue experiments in GC cells. The sponge of circORC5 with miR-30c-2-3p was confirmed by luciferase gene report and RNA immunoprecipitation assays. The expression, localization and prognosis of circORC5 in GC were evaluated by fluorescence in situ hybridization. The effects of METTL14 and (or) circORC5 on miR-30c-2-3p-mediated AKT1S1 and EIF4B were estimated by RT-qPCR and Western blot analyses.
Results
We found that METTL14 was downregulated in GC tissue samples and its low expression acted as a prognostic factor of poor survival in patients with GC. Ectopic expression of METTL14 markedly repressed growth and invasion of GC cells
in vitro
and
in vivo
, whereas knockdown of METTL14 harbored the opposite effects. Mechanically, m
6
A-circRNA epitranscriptomic microarray and Me-RIP identified circORC5 as the downstream target of METTL14. Silencing of METTL14 reduced the m
6
A level of circORC5, but increased circORC5 expression. Moreover, circORC5 could sponge miR-30c-2-3p, and reverse METTL14-caused upregulation of miR-30c-2-3p and downregulation of AKT1S1 and EIF4B. In addition, circORC5 possessed a negative correlation with miR-30c-2-3p and indicated a poor survival in GC.
Conclusion
Our findings demonstrate that METTL14-mediated m
6
A modification of circORC5 suppresses gastric cancer progression by regulating miR-30c-2-3p/AKT1S1 axis.
Journal Article
Alhagi sparsifolia acclimatizes to saline stress by regulating its osmotic, antioxidant, and nitrogen assimilation potential
2022
Background
Alhagi sparsifolia (Camelthorn)
is a leguminous shrub species that dominates the Taklimakan desert’s salty, hyperarid, and infertile landscapes in northwest China. Although this plant can colonize and spread in very saline soils, how it adapts to saline stress in the seedling stage remains unclear so a pot-based experiment was carried out to evaluate the effects of four different saline stress levels (0, 50, 150, and 300 mM) on the morphological and physio-biochemical responses in
A. sparsifolia
seedlings.
Results
Our results revealed that N-fixing
A. sparsifolia
has a variety of physio-biochemical anti-saline stress acclimations, including osmotic adjustments, enzymatic mechanisms, and the allocation of metabolic resources. Shoot–root growth and chlorophyll pigments significantly decreased under intermediate and high saline stress. Additionally, increasing levels of saline stress significantly increased Na
+
but decreased K
+
concentrations in roots and leaves, resulting in a decreased K
+
/Na
+
ratio and leaves accumulated more Na + and K + ions than roots, highlighting their ability to increase cellular osmolarity, favouring water fluxes from soil to leaves. Salt-induced higher lipid peroxidation significantly triggered antioxidant enzymes, both for mass-scavenging (catalase) and cytosolic fine-regulation (superoxide dismutase and peroxidase) of H
2
O
2
. Nitrate reductase and glutamine synthetase/glutamate synthase also increased at low and intermediate saline stress levels but decreased under higher stress levels. Soluble proteins and proline rose at all salt levels, whereas soluble sugars increased only at low and medium stress. The results show that when under low-to-intermediate saline stress, seedlings invest more energy in osmotic adjustments but shift their investment towards antioxidant defense mechanisms under high levels of saline stress.
Conclusions
Overall, our results suggest that
A. sparsifolia
seedlings tolerate low, intermediate, and high salt stress by promoting high antioxidant mechanisms, osmolytes accumulations, and the maintenance of mineral N assimilation. However, a gradual decline in growth with increasing salt levels could be attributed to the diversion of energy from growth to maintain salinity homeostasis and anti-stress oxidative mechanisms.
Journal Article
Nutrient recovery from anaerobic digestion of food waste: impacts of digestate on plant growth and rhizosphere bacterial community composition and potential function in ryegrass
by
Abbott, Lynette K
,
You-Cai, Xiong
,
Mickan, Bede S
in
Abundance
,
Agricultural practices
,
Ammonia
2020
Global food wastage equates to about 1.3 billion tons per year, which causes serious environmental impacts. The objective of this study was to evaluate the influences of addition of digestate from food waste in comparison to a synthetic liquid urea ammonium nitrate solution on plant growth, rhizosphere bacterial community composition and diversity, and hyphal abundance of arbuscular mycorrhizal (AM) fungi. Plant and soil samples were collected at 25, 50, and 75 days after seedling emergence. Annual ryegrass growth was significantly increased by both liquid urea ammonium nitrate and digestate, and digestate was just as effective as liquid urea ammonium nitrate. Additionally, digestate (50 kg N ha−1) significantly increased AM fungal hyphae density. Liquid urea ammonium nitrate (50 kg N ha−1) significantly decreased AM fungal hyphae density compared with liquid urea ammonium nitrate (25 kg N ha−1) at DAE 75. Digestate and liquid urea ammonium nitrate applications significantly shifted the bacterial community composition and OTU richness and changed the abundance of microbial C and N-cycling genes, while application rates had no significant effect. Structural equation modeling showed that digestate and UAN addition both directly and indirectly affected bacterial, C and N cycling genes community composition; the indirect effects were related to increased soil NO3− content and reduced pH. This study showed that the use of digestate as a soil amendment can be environmentally effective and can provide a sustainable supply of nutrients that increases soil organic C. Moreover, the use of digestate can readily be incorporated into agricultural practices with potentially less impact on soil microflora diversity and function than conventional fertilizers.
Journal Article
Epigenetic suppression of GAD65 expression mediates persistent pain
2011
Identification of the mechanisms that drive the transition from acute to chronic pain could lead to new treatments. Now, Zhizhong Pan and colleagues demonstrate that chronic pain causes epigenetic downregulation of GAD65 and results in inhibitory neurotransmission deficits in the brainstem of rats.
Chronic pain is a common neurological disease involving lasting, multifaceted maladaptations ranging from gene modulation to synaptic dysfunction and emotional disorders. Sustained pathological stimuli in many diseases alter the output activities of certain genes through epigenetic modifications, but it is unclear how epigenetic mechanisms operate in the development of chronic pain. We show here that in the rat brainstem nucleus raphe magnus, which is important for central mechanisms of chronic pain, persistent inflammatory and neuropathic pain epigenetically suppresses
Gad2
(encoding glutamic acid decarboxylase 65 (GAD65)) transcription through histone deacetylase (HDAC)-mediated histone hypoacetylation, resulting in impaired γ-aminobutyric acid (GABA) synaptic inhibition.
Gad2
knockout mice showed sensitized pain behavior and impaired GABA synaptic function in their brainstem neurons. In wild-type but not
Gad2
knockout mice, HDAC inhibitors strongly increased GAD65 activity, restored GABA synaptic function and relieved sensitized pain behavior. These findings suggest GAD65 and HDACs as potential therapeutic targets in an epigenetic approach to the treatment of chronic pain.
Journal Article
Natural killer cell homing and trafficking in tissues and tumors: from biology to application
2022
Natural killer (NK) cells, a subgroup of innate lymphoid cells, act as the first line of defense against cancer. Although some evidence shows that NK cells can develop in secondary lymphoid tissues, NK cells develop mainly in the bone marrow (BM) and egress into the blood circulation when they mature. They then migrate to and settle down in peripheral tissues, though some special subsets home back into the BM or secondary lymphoid organs. Owing to its success in allogeneic adoptive transfer for cancer treatment and its “off-the-shelf” potential, NK cell-based immunotherapy is attracting increasing attention in the treatment of various cancers. However, insufficient infiltration of adoptively transferred NK cells limits clinical utility, especially for solid tumors. Expansion of NK cells or engineered chimeric antigen receptor (CAR) NK cells ex vivo prior to adoptive transfer by using various cytokines alters the profiles of chemokine receptors, which affects the infiltration of transferred NK cells into tumor tissue. Several factors control NK cell trafficking and homing, including cell-intrinsic factors (e.g., transcriptional factors), cell-extrinsic factors (e.g., integrins, selectins, chemokines and their corresponding receptors, signals induced by cytokines, sphingosine-1-phosphate (S1P), etc.), and the cellular microenvironment. Here, we summarize the profiles and mechanisms of NK cell homing and trafficking at steady state and during tumor development, aiming to improve NK cell-based cancer immunotherapy.
Journal Article
Moisture- and period-dependent interactive effects of plant growth-promoting rhizobacteria and AM fungus on water use and yield formation in dryland wheat
by
Zhu, Ying
,
Iqbal, Awais
,
Wang, Wei
in
1-aminocyclopropane-1-carboxylate deaminase
,
1-aminocyclopropane-1-carboxylic acid
,
Agricultural research
2024
Purpose
In drought-prone soils, plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungus (AMF) might positively affect water uptake and crop yield via rhizosphere interactions.
Methods
Sole and combined additions of
Bacillus amyloliquefaciens
producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and
Rhizophagus irregularis
into rhizospheric soils were performed under well-watered (WW; 80% field water capacity), moderate water stress (MWS; 50% FWC) and severe water stress (SWS; 35% FWC) in pot-cultured wheat (
Triticum aestivum
L.).
Results
In moderate and severe drought stress, water use efficiency (WUE
B
) was increased by 27.9–34.3% in PGPR and 20–22.1% in AMF treatments, respectively, and grain yield was improved by 20.03–30.77% in PGPR and 12.13–34.34% in AMF treatments, respectively, compared with control (CK). Importantly, the co-inoculation of AMF and PGPR significantly promoted WUE
B
by 11.12–27.77% and grain yield by 18.26–21.68% compared to the average value of two sole inoculations in MWS and SWS treatments, respectively. WUE
Y
and biomass production followed a similar trend as WUE
B
and yield. Particularly, the above parameters were significantly enhanced with the prolonged developmental stages (
p
< 0.05). ACC deaminase significantly reduced ACC accumulation in MWS and SWS, enhanced AMF root colonization, and promoted rhizosphere microbial biomass carbon and nitrogen levels across all three developing stages. Furthermore, AMF-PGPR co-inoculation enhanced chlorophyll and carotenoid contents during anthesis while reducing them during pre-harvesting. Enhanced water uptake and root activities upsurged photosynthetic traits throughout the growing season.
Conclusion
AMF-PGPR co-inoculation acted as a promising solution to cope with the droughted environment via root activities for stronger water capture.
Journal Article
Efficient biosynthesis of nucleoside cytokinin angustmycin A containing an unusual sugar system
2021
Angustmycin A has anti-mycobacterial and cytokinin activities, and contains an intriguing structure in which an unusual sugar with C5′-C6′ dehydration is linked to adenine via an
N
-glycosidic bond. However, the logic underlying the biosynthesis of this molecule has long remained obscure. Here, we address angustmycin A biosynthesis by the full deciphering of its pathway. We demonstrate that AgmD, C, A, E, and B function as
d
-allulose 6-phosphate 3-epimerase,
d
-allulose 6-phosphate pyrophosphokinase, adenine phosphoallulosyltransferase, phosphoribohydrolase, and phosphatase, respectively, and that these collaboratively catalyze the relay reactions to biosynthesize angustmycin C. Additionally, we provide evidence that AgmF is a noncanonical dehydratase for the final step to angustmycin A via a self-sufficient strategy for cofactor recycling. Finally, we have reconstituted the entire six-enzyme pathway in vitro and in
E. coli
leading to angustmycin A production. These results expand the enzymatic repertoire regarding natural product biosynthesis, and also open the way for rational and rapid discovery of other angustmycin related antibiotics.
Angustmycin A is a nucleoside antibiotic having anti-mycobacterial and cytokinin activities. Here, the authors report the whole pathway leading to angustmycin A biosynthesis in
Streptomyces
and achieve the heterologous production of angustmycin A in
E. coli
.
Journal Article