Biology subjects

Borges, R. M.

Publications and source records attributed to Borges, R. M..

9 recordsLinked to original sources

bioRxiv2026

Higher Lipid Saturation in Well-Irrigated Georgia Cotton Plants: A Field-Based NMR Metabolomics Study

Cotton (Gossypium hirsutum) is an economically important crop, but it faces increasing pest outbreaks, especially in non-irrigated areas. In this study, 20 cotton farms using center-pivot irrigation were sampled in southern Georgia to assess chemical differences between non-irrigated and irrigated areas. Proton (1H) nuclear magnetic resonance (NMR) data were obtained from cotton leaves, and Principal Component Analysis (PCA) was performed to assess differences in chemical composition. Across all samples, farm site accounted for most of the variability, but within each farm site, the PCA scores plots showed clear separation between non-irrigated and irrigated conditions in 10 sites. Inspecting the PCA loadings revealed significant resonances resembling a lipid-like signal. After reverse-phase fractionation, we observed that many of these resonances appeared together in later fractions, suggesting a lipid, specifically a fatty acid such as linoleic acid. We hypothesized that differences in net lipid saturation level may drive separation between non-irrigated and irrigated samples. Six farm sites had a significantly or marginally significantly higher degree of unsaturation in irrigated samples, while one farm site had significantly higher unsaturation in non-irrigated samples. Our results indicate that drought stress likely affects lipid profile composition, which could be driving higher herbivorous pest densities in drought-stressed crops.

plant biology↗

bioRxiv2025

Metabolite Fraction Libraries for Quantitative NMR Metabolomics

Nuclear Magnetic Resonance (NMR) has unique strengths in metabolomics studies, particularly in quantifying mixtures and elucidating the structures of unknown molecules. One-dimensional (1D) proton (1H) NMR is the most common method; however, spectral overlap is significant, making analysis challenging. We present a new approach that utilizes chromatographically separated fractions from a pooled sample, henceforth called a metabolite fraction library (mFL). We developed an algorithm to extract highly correlated peaks from the mFL, collectively forming a metabolite basis set (mBS). The mBS can be fit to NMR profiling data, enabling comprehensive quantification. Applied to 10 mixtures of 53 metabolites, our approach accurately quantified 50, quantified an impurity and an oxidation product, and described between 91-96% of total spectral intensity. The method is demonstrated using the fungus Neurospora crassa, resulting in the identification of 45 metabolites with high confidence, 45 with medium confidence, and accounting for 94% of total spectral intensity.

bioinformatics↗

bioRxiv2025

Ancient bridges, modern threat: Conserving landscape heterogeneity ensures sustenance of living root-bridges in Meghalaya

The Anthropocene, marked by rapid biodiversity loss, has renewed attention on natures contributions to people, which include ecological, cultural, and spiritual values. A striking example of such nature-culture interactions are the living root-bridges of Meghalaya, India, where Khasi people ingeniously train the aerial roots of Ficus elastica across river valleys to form natural bridges. These structures, currently under consideration for UNESCO World Heritage recognition, exemplify sustainable resource use in one of the wettest and most landslide-prone regions of the world. However, increasing tourism and unregulated construction is threatening to this nature culture relationship in a biodiversity hotspot. In such situations, understanding the factors governing the geneflow is vital to the preservation of interactions between the pollinating fig wasps, the fig tree and its seed dispersers. Despite its ecological and cultural significance, little is known about the population biology or dispersal potential of F. elastica. Here, we investigated dispersal potential of natural populations of F. elastica across Meghalaya. Using ddRAD-SNP genotyping ([~]12K SNPs from 308 individuals), we detected four genetic clusters corresponding to E. Khasi, W. Khasi, W. Jaintia, and Ribhoi hills. Redundancy analysis and resistance modelling revealed that wind regimes and topography jointly structure these populations, enabling gene flow within but not across river valleys. Analysis of spatial distribution of related individuals indicates short dispersal distance of 1-4km varying across different populations. Given F. elasticas association with riparian ecosystems, and with UNESCO recognition pending, our study underscores the need for strict guidelines to curb habitat destruction and ensure the long-term survival of both the species and its cultural legacy.

ecology↗

bioRxiv2024

PyINETA: Open-source platform for INADEQUATE-JRES integration in NMR metabolomics

Annotating compounds with high confidence is a critical element in metabolomics. 13C-detection NMR experiment INADEQUATE (incredible natural abundance double-quantum transfer experiment) stands out as a powerful tool for structural elucidation, whereas this valuable experiment is not often included in metabolomics studies. This is partly due to the lack of community platform that provides structural information based INADEQUATE. Also, it is often the case that a single study uses various NMR experiments synergistically to improve the quality of information or balance total NMR experiment time, but there is no public platform that can integrate the outputs of INADEQUATE and other NMR experiments either. Here, we introduce PyINETA, Python-based INADEQUATE network analysis. PyINETA is an open-source platform that provides structural information of molecules using INADEQUATE, conducts database search, and integrates information of INADEQUATE and a complementary NMR experiment 13C J-resolved experiment (13C-JRES). Those steps are carried out automatically, and PyINETA keeps track of all the pipeline parameters and outputs, ensuring the transparency of annotation in metabolomics. Our evaluation of PyINETA using a model mouse study showed that our pipeline successfully integrated INADEQUATE and 13C-JRES. The results showed that 13C-labeled amino acids that were fed to mice were transferred to different tissues, and, also, they were transformed to other metabolites. The distribution of those compounds was tissue-specific, showing enrichment of particular metabolites in liver, spleen, pancreas, muscle, or lung. The value of PyINETA was not limited to those known compounds; PyINETA also provided fragment information for unknown compounds. PyINETA is available on NMRbox.

systems biology↗

bioRxiv2023

Sensing volatiles throughout the body: Geographic and tissue-specific olfactory receptor expression in the fig wasp Ceratosolen fusciceps

An essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species, Ceratosolen fusciceps, a specialist wasp pollinator of Ficus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny of Ceratosolen ORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the antennae, 20 percent were also expressed in non-antennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts of C. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of OR expression of C. fusciceps in widely separated geographical locations, i.e., south (urban) and northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.

genomics↗

bioRxiv2022

A Universal Language for Finding Mass Spectrometry Data Patterns

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.

bioinformatics↗

bioRxiv2022

An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

Large-scale untargeted metabolomics studies suffer from individual variation, batch effects and instrument variability, making comparisons of common spectral features across studies difficult. One solution is to compare studies after compound identification. However, compound identification is expensive and time consuming. We successfully identify common spectral features across multiple studies, with a generalizable experimental design approach. First, we included an anchor strain, PD1074, during sample and data collection. Second, we collected data in blocks with multiple controls. These anchors enabled us to successfully integrate three studies of Caenorhabditis elegans for nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) data from five different assays. We found 34% and 14% of features to be significant in LC-MS and NMR, respectively. Between 20-50% of spectral features differ in a mutant and among a set of genetically diverse natural strains, suggesting this reduced set of spectral features are excellent targets for compound identification. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/485859v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@84abe1org.highwire.dtl.DTLVardef@3066fforg.highwire.dtl.DTLVardef@1ba166corg.highwire.dtl.DTLVardef@164cf0_HPS_FORMAT_FIGEXP M_FIG C_FIG Fourteen C. elegans strains are used in three individual studies. PD1074, the anchor control strain (orange), is grown alongside test strains (green, yellow, purple). Multiple biological replicates of PD1074 captures environmental variation in growth conditions. Non-polar and polar metabolic data across the three studies (i.e., natural strains, central metabolism mutants, and UGT mutants) were collected by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Data acquisition controls in each block included biological reference material and pooled PD1074 samples. Biological replicates of PD1074 (n = 42 for LC-MS, n = 52 for NMR) were included in all batches. Meta-analysis provided comparable inferences to mixed effects models, and the estimated relative effects of each test strain to PD1074 and straightforward comparisons of test strains across experiments.

systems biology↗

bioRxiv2021

Three new species of nematodes from the syconia of Ficus racemosa in southern India

SummaryFicus racemosa with an Indo-Australasian distribution, has so far been recorded to harbour in its fruits, nematode species of the aphelenchoid genera Schistonchus, Ficophagus and Martininema, and species of diplogastrid genera Teratodiplogaster and Pristionchus. The Indian species reported so far from Ficus racemosa lack comprehensive details on morphology and molecular characterization. In this paper, we describe three new species of nematodes obtained from syconia (enclosed globular infructescence or fruit) of Ficus racemosa found in southern India. Ficophagus glomerata n. sp. is characterised by small body having b=5.2-9.6, c= 18-23; slightly set-off lip region having well developed cephalic framework; secretory-excretory pore opens near the head; slender stylet with small, rounded/ sloping knobs; ovoid median bulb with relatively posteriorly-placed valve plates; males with sickle-shaped spicules having spatulate or hammer-shaped capitulum, represented by an elongate-ovoid condylus and long digitate rostrum and tail conoid with fine, hair-like terminal spike. Teratodiplogaster glomerata n. sp. is characterised by long tubular and narrow stoma with fractal pieces in prostegostom; long rectangular metacorpus; female reproductive system with conspicuous spermatheca and amoeboid sperms; males having short, arcuate spicules and keeled gubernaculum; genital papillae in the configuration of P1, P2, C, P3, P4, P5d, (P6d, P7), P8d, Ph and tail conoid with a terminal or subterminal mucro. Pristionchus glomerata n. sp. is characterised by four morphotypes mainly with variations in lip region, stoma, spicules, gubernaculum, and the position of genital papillae. Phylogenetic analyses based upon near-full-length small subunit (SSU) and D2-D3 expansion segments of large subunit (LSU) rRNA genes confirmed affinities with sister species of corresponding genera.

zoology↗

bioRxiv2020

Staying in the club: Exploring criteria governing metacommunity membership for obligate symbionts under host-symbiont feedback

O_LIMetacommunity membership is influenced by habitat availability and trophic requirements. However, for multitrophic symbiont communities that are closely associated with host plants, symbionts and hosts may additionally influence each other affecting membership criteria in novel ways. For example, failure of beneficial services from a symbiont could elicit a response from the host that impacts the entire community. Understanding such host-symbiont feedback effects on symbiont community membership can be crucial for understanding symbiont community structure and function. C_LIO_LIWe investigate membership for a multitrophic insect symbiont community where symbionts colonize host inflorescences during specific developmental stages termed colonization windows. Inflorescences are host-derived organs and serve as habitat microcosms. Symbionts exhibit a diversity of interactions ranging from mutualism to parasitism. Hosts exhibit immediate feedback by aborting inflorescences not pollinated by mutualistic symbionts and habitats are consequently lost for all other symbiont species. Using relevant empirically measured microcosm parameters, we simulate symbiont dispersal from and colonization of other host inflorescences. We vary host densities and symbiont colonization window lengths, and track the persistence of each symbiont species in the metacommunity based on the temporal availability of the resource and the trophic position of the symbiont. C_LIO_LISince the persistence of the microcosm habitat is dictated by pollination performed by the mutualist, the mutualist fares better than all other symbionts. For prey, the length of colonization windows was positively related with colonization success and symbiont persistence. For predators, the cumulative length of the colonization windows of their prey dictated their success; diet breadth or prey colonization success did not influence the persistence of predators. Predators also had a greater host-plant density requirement than prey for persistence in the community. These results offer valuable insights into host density requirements for maintaining symbionts, and have implications for multitrophic symbiont community stability. C_LIO_LISynthesis. Factors influencing symbiont community membership can be unique when host-symbiont feedback impacts host microcosm development. Special constraints can govern symbiont community membership, function and structure and symbiont persistence in such metacommunities. C_LI

ecology↗