With the Generative Pre-trained Transformer 3.5 (GPT-3.5) exhibiting remarkable reasoning and comprehension abilities in Natural Language Processing (NLP), most Question Answering (QA) research has primarily centered around general QA tasks based on GPT, neglecting the specific challenges posed by Complex Table QA. In this paper, we propose to incorporate GPT-3.5 to address such challenges, in which complex tables are reconstructed into tuples and specific prompt designs are employed for dialogues. Specifically, we encode each cell's hierarchical structure, position information, and content as a tuple. By enhancing the prompt template with an explanatory description of the meaning of each tuple and the logical reasoning process of the task, we effectively improve the hierarchical structure awareness capability of GPT-3.5 to better parse the complex tables. Extensive experiments and results on Complex Table QA datasets, i.e., the open-domain dataset HiTAB and the aviation domain dataset AIT-QA show that our approach significantly outperforms previous work on both datasets, leading to state-of-the-art (SOTA) performance.

Large Language Models are Complex Table Parsers

So called ‘drop-in’ Biofuels produced from plants are becoming increasingly important for the aviation and shipping industries, which urgently need to move away from fossil fuels in order to limit their impact on the climate. Algae farms provide a number of benefits over traditional biofuel crops, such as sugar cane, by alleviating competition for arable land. When exposed to high light, the green alga Chlamydomonas reinhardtii produces triacylglycerols (TAGs) which can be converted to drop-in biodiesel. Excess light results in the over-reduction of the photosynthetic electron transport chain, and it has been suggested that the production of TAGs is in response to this redox imbalance. A deeper understanding, therefore, of how Chlamydomonas cells address redox imbalance will help to inform future work aiming to maximise TAG production in these conditions. Our work has highlighted a potential role for the phenomenon known as light enhanced respiration (LER) in responding to redox stress induced by high light. We show that presence of acetate in the growth media may allow cells to better acclimate to high light by increasing the capacity of the cells for LER. Autotrophic cells (cells grown without acetate) appear to be more susceptible to photodamage than mixotrophic (grown with acetate) when grown in high light. Our results display the complexity of the high light response and provide preliminary evidence for the potential of the mitochondria as a tool for addressing redox imbalance. 

A role for mitochondria during high light stress in Chlamydomonas reinhardtii

Mitochondria are most known for their role in energy production, but they are also implicated in many other cellular functions (apoptosis, ROS production, cell proliferation, aging). In humans, the mitochondrial DNA was believed to encode only 37 genes involved in energy production and mitochondrial translation. However, recent studies have shown that within these genes could hide several small alternative genes (genes with translation initiation or termination sequences distinct from the reference gene sequences in which they are found) coding for micropeptides with a broad spectrum of functions that can be newly added to the large list of functions in which mitochondria are involved.

Following the discovery of the mitochondrial alternative gene mtaltnd4, we try to elucidate the functions of the gene and its peptide (MTALTND4) by studying: (1) the expression pattern of the peptide in different human tissues and blood plasma, (2) the involvement of the gene in the major mitochondrial functions by exposing cells to various treatments, (3) the interaction partners of MTALTND4 by mass spectrometry and (4) the impact of the peptide on cell transcriptome. 

We have found that mtaltnd4 may potentially produce a signaling protein in response to stress that would regulate certain cell metabolic processes and there is surely more to discover.











The alternative gene mtaltnd4: uncovering the mitochondria’s hidden functions

Polyploids are of common occurrence among the plants. Several studies have been conducted to understand the impact of polyploidy on the evolution of plant genome. Natural polyploids do occur in the wild, but it is difficult to decipher which changes are due to polyploidy as the plants accumulate variation over the history of their existence. It is important to study the impact of polyploidy away from natural variation. Therefore, we generated synthetic neoautopolyploids in two species of Vigna L. using colchicine-based cotton swab method. The polyploids were screened via flowcytometry and confirmed polyploids were taken to the field to study biological parameters. The two species were found to be behaving differently based on various parameters like photosynthetic efficiency, cell density, stomatal count, cell size and nucleus size. We will be studying inheritance pattern of these traits in subsequent generations. Our study provides a proof that polyploidy does not always have a positive scaling effect on plants at various biological parameters and the changes are species specific. We will be studying genomic changes in future and will correlate them with morphological changes observed.  

Keywords: Polyploids, WGD, Autopolyploid, Flowcytometry, morphometery

Whole Genome Duplication Show Species-Specific Morphological Changes In Neoautopolyploids

Sessile benthic species are submitted to fluctuating oxygen and temperature conditions that can negatively affect their energy and redox balance. Single effects of temperature and oxygen fluctuations have been extensively studied, but their combined effects are not yet well understood. We studied the bioenergetics and oxidative stress markers in the Pacific oyster Crassostrea gigas exposed for 10 days to daily immersion-emersion cycles under the control (15°C) (H), elevated (30°C) (HW), and fluctuating (15°C in water and 30°C in air) (HF) temperature. Oysters maintained under normoxia and 15°C were used as controls. Mortality increased in the oysters exposed to hypoxia and elevated temperature indicating acute thermal stress. Oysters co-exposed to fluctuating oxygen and temperature showed a decrease in the mitochondrial aerobic capacity but no onset of anaerobiosis shown by the lack of succinate accumulation. Glycogen content decreased in the digestive gland, whereas protein content increased in the gill of the HF group indicating higher protein deposition combined with higher energy demand during reoxygenation. In contrast, the HW group showed decreased protein levels reflecting heat-induced suppression of protein synthesis. Lipid peroxidation levels were elevated in the gills of the oysters from HW (but not H or HF group) indicating that antioxidant systems of oysters can cope with hypoxia-induced oxidative stress under the normal or fluctuating temperature but not during constant warming. Thus, long-term warming combined with intermittent hypoxia can lead to breakdown of physiological functions and higher summer mortality like already observed in the German Wadden Sea.

Effects of fluctuating oxygen and temperature regime on bioenergetics and oxidative stress of the pacific oyster Crassostrea gigas

Microsphere super-resolution microscopy has recently received a lot of attention due to its simplicity and its capability to resolve features beyond the diffraction limit for living systems, in real time, without being invasive. Current systems which are able to image small biological structures are destructive, invasive (they use fluorescent dyes) or they provide reconstructed images (i.e. not a real time imaging of living organisms). The authors designed and built a bio-microscope tailored around the SMAL® (Super-Resolution Microsphere Amplifying Lens) objective lens which overcomes these drawbacks. The novelty of the setup is the ability to study cell’s structures and viruses which previously were not possible to be imaged using conventional white light microscopy. In this work, along various plant cells, label-free tobacco mosaic virus was employed for imaging in this work due to its stability, reliability, and its dimensions beyond the diffraction limit. The results were compared with images obtained using an X100/1.40 NA oil immersion objective lens fitted onto a white light microscope, in the same location. Microsphere assisted microscopy is a novel type of optical microscopy with great potential for high resolution imaging of in vivo biological structures and pathogens.

Optical super-resolution imaging of tissues and tobacco mosaic virus (TMV) using microsphere technology

Mammalian cell culture is a fundamental tool used to study living cells. Presently, the standard protocol for performing cell culture involves the use of commercial media that contain an excess of nutrients to prevent depletion during experiments. While this reduces the likelihood of cell starvation, it creates non-physiological culture conditions that have been shown to ‘re-wire’ cellular metabolism and broadly influence cell physiology. Recently, researchers have developed physiological media like Plasmax, formulated to approximate the nutrient composition of human blood plasma. Although this represents an improvement in cell culture practice, such physiologic media may be vulnerable to nutrient depletion over the course of an experiment  extending over several days. In this study we directly addressed this concern by measuring the rates of glucose and amino acid depletion from Plasmax by several cancer cell lines (PC3, LNCaP, MCF-7 and SH-SY5Y) over 48 hours. In all cell lines, depletion of glucose from Plasmax was rapid such that, by 48h, cells were hypoglycemic (less than 2mM glucose). Most amino acids were similarly rapidly depleted to sub-physiological levels by 48h. In contrast, glucose and most amino acids remained within the physiological range at 24h. Using RNA sequencing, we show that this nutrient depletion is associated with enrichment of cellular starvation responses, amino acid biosynthesis, apoptotic signalling, and endoplasmic reticulum stress response. Alterations in mitochondrial respiration using Seahorse extracellular flux analysis were also observed. Taken together, these results exemplify the metabolic considerations for Plasmax use, highlighting that cell culture in Plasmax requires daily media exchange.

Rapid nutrient depletion by cancer cells cultured in the physiologic medium Plasmax  

Programmed cell death (PCD) is a genetically managed biological process that results in the targeted sacrifice of unwanted or diseased cells. Plants use PCD for various purposes such as development, defence against pathogens, response to abiotic stress caused by UV radiation or heat shock. Several proteinases are involved in the PCD process; among them, cathepsin B (CathB) which plays an important role in pathogen defence, plant development, germination, senescence, microspore embryogenesis and abiotic stress response. A greater understanding of the molecular mechanisms underlying the processes downstream of CathB is the next important step for new discoveries in cell biology and applications in biotechnology. To achieve this goal, it is important to discover and test substrates cleaved by plant CathB. Up to 13 substrates for CathB were identified in animal cells, and we found orthologous genes in Arabidopsis thaliana for eight of them. Among these, we are testing some candidate substrates for CathB. To experimentally validate the cleavage site, we used leaf agro-infiltration to co-expressed substrate GFP-fusion and CathB in tobacco cells and carried out cleavage assays. in vivo and in vitro results will be presented. 
















Characterising the proteolytic network of plant cathepsin B

Membrane trafficking and organelle biogenesis play important roles in plant growth and development, as well as responses to external signals. The plant endomembrane system contains several functionally distinct membrane-enclosed organelles, including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosomes (EE), prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. One of our major research programs has been focused on illustrating the underlying mechanisms of vacuolar trafficking and vacuole biogenesis and function in plant cells. One major approach has been the whole-cell electron tomography (ET) analysis with nanometer resolution of vacuole formation and distribution in different cell types of developmental stages, including root cells, stomatal lineage cells and developing pollens in Arabidopsis. Here I will present our recent work and models of vacuole biogenesis and function in plants from the ET analysis. Supported by grants from the Research Grants Council of Hong Kong and CUHK. 

Whole-cell Electron Tomography Analysis of Vacuoles in Plant Cells

The vacuole is a hallmark of the plant cell, generating turgor pressure and thus driving growth. Seed plant embryos also contain numerous specialised Protein Storage Vacuoles (PSV) which are repositories for the nutritional content of seeds. But how do these specialised PSVs form and what mechanism drives this process? Recent work has demonstrated that PSVs are formed by the remodelling of the single embryonic vacuole into many fragmented PSVs. The main constituent of these PSV are seed storage proteins (SSP).  We have shown that SSP undergo liquid-liquid phase separation forming a droplet within the vacuole and these SSP droplets can bend the tonoplast membrane. However, can this process of SSP phase separation drive fragmentation of a single embryonic vacuole into multiple PSV? Additionally, which proteins and conditions drive phase separation of SSP in the embryonic vacuole? We have identified and are characterising protein candidates for drivers of phase separation in the embryonic vacuole and determining their role in PSV biogenesis.

Its all just a phase: Phase separation driving organelle biogenesis.

Mitochondria possess a genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is limited to 37 genes, with little room for evolutionary novelties. This is radically different from bacterial genomes, which are much larger, and in which we can find genes inside other genes. These sequences are called alternatives open reading frames or altORFs, and they have key functions. By ignoring altORFS, have we underestimated the coding potential of the mitogenome? We found a downstream alternative ATG initiation codon in the +3 reading frame of the human mitochondrial nd4 gene. This newly characterized mitochondrial altORF encodes a 99-amino acids long polypeptide termed MTALTND4 with a completely different amino acid sequence from ND4. MTALTND4 is localized in mitochondria and is also found in the plasma, and it impacts mitochondrial physiology. These findings indicate that mitochondrial genes in humans (and other species) have gone unnoticed. This calls into question the evolution of the mitochondrial genome as well as the selection pressures exerted on the mitochondria and the mechanisms allowing the translation of these alternative proteins. We anticipate that more studies on the alternative mitochondrial proteome will expedite the discovery of new mitochondrial genes with key biological roles.

The underestimated protein coding potential of the mitochondrial genome

Birds metabolically remodel their flight muscle prior to migration to meet the high energetic demands of migratory flight. The degree of plasticity mediated by changes in mitochondrial function is poorly understood but could be explained by two non-mutually exclusive hypotheses: variation in mitochondrial quantity or individual mitochondrial function. For each hypothesis, we predicted higher mitochondrial abundance and predict higher substrate oxidative capacity and reduced reactive oxygen species formation during migration, respectively. We evaluated both hypotheses using yellow-rumped warblers (Setophaga coronata) captured during their autumn migration at Long Point, Ontario, Canada. Half of the birds were sampled in the migratory phenotype and the remaining birds were transferred to a short day photoperiod (9L:15D) and sampled in a non-migratory phenotype. We measured mitochondrial abundance via citrate synthase maximal activity in the pectoralis major flight muscle. We investigated mitochondrial function via high-resolution fluororespirometry on isolated pectoralis mitochondria. We measured O2 consumption and H2O2 formation rates from oxidation of lipid and carbohydrate substrates. We also measured oxygen consumption specific to electron transport system protein complexes using complex-specific substrates and inhibitors. Citrate synthase activity and mitochondrial respiration for each substrate and complexes II, III and IV was higher in the migratory phenotype, yet H2O2 formation rates were similar between phenotypes. These data suggest that pectoralis mitochondrial abundance and oxidative capacity are elevated during migration without increasing reactive oxygen species formation. Our findings support both hypotheses and indicate that mitochondrial function mediates seasonal metabolic plasticity in the pectoralis flight muscle of migratory songbirds.

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Large Language Models are Complex Table Parsers

A role for mitochondria during high light stress in Chlamydomonas reinhardtii

The alternative gene mtaltnd4: uncovering the mitochondria’s hidden functions

Whole Genome Duplication Show Species-Specific Morphological Changes In Neoautopolyploids

Effects of fluctuating oxygen and temperature regime on bioenergetics and oxidative stress of the pacific oyster Crassostrea gigas

Optical super-resolution imaging of tissues and tobacco mosaic virus (TMV) using microsphere technology

Rapid nutrient depletion by cancer cells cultured in the physiologic medium Plasmax

Characterising the proteolytic network of plant cathepsin B

Whole-cell Electron Tomography Analysis of Vacuoles in Plant Cells

Its all just a phase: Phase separation driving organelle biogenesis.

The underestimated protein coding potential of the mitochondrial genome

Flight muscle mitochondria are seasonally plastic in a migratory songbird

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