Biology subjects

Paulino, J.

Publications and source records attributed to Paulino, J..

3 recordsLinked to original sources

bioRxiv2026

Associations of waterbirds with harvesting and ploughing events in rice fields: increasing foraging opportunities or just gathering for the feast?

Surges in food availability create localized but intense foraging opportunities, often attracting multi-species consumer groups. Agricultural practices can trigger these surges, prompting bird associations. However, the strength and duration of the association, as well as its drivers, remain unclear. This study examines waterbird association with harvesting and ploughing events in rice fields. The duration and magnitude of these associations were determined and three hypotheses addressed to explain them: (1) increased food availability, (2) enhanced foraging success and (3) reduced time allocated to vigilance. Waterbird counts and GPS tracking revealed strong associations with management events. Bird numbers spiked during events but declined within one to two days. Food availability (and soil penetrability) increased significantly during events - crayfish and rice during harvesting, worms and soil penetrability during ploughing - supporting Hypothesis 1. However, this did not improve foraging performance (intake rate, foraging success), rejecting Hypothesis 2. Higher competition, interference or kleptoparasitism in these large mixed-species flocks may offset increased food availability benefits. Alternatively, functional responses of target species may limit prey intake due to physiological or behavioural constraints. Hypothesis 3 was also unsupported, as birds did not reduce vigilance. It is plausible that birds may be drawn to events by the perception of a feast, not actual benefits. Gregariousness and foraging behaviour by "local enhancement" may explain such associations. Results highlight the complexity of bird responses to food surges while suggesting waterbirds in rice fields maintain stable foraging performance during agricultural management events and otherwise, indicating resilience to agricultural timing shifts.

ecology↗

bioRxiv2024

Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct expression patterns and potential markers of progression

In order to advance our understanding of precancers in the pancreas, 69 pancreatic intraductal papillary neoplasms (IPNs), including 64 intraductal papillary mucinous neoplasms (IPMNs) and 5 intraductal oncocytic papillary neoplasms (IOPNs), 32 pancreatic cyst fluid samples, 104 invasive pancreatic ductal adenocarcinomas (PDACs), 43 normal adjacent tissues (NATs), and 76 macro-dissected normal pancreatic ducts (NDs) were analyzed by mass spectrometry. A total of 10,246 proteins and 22,284 glycopeptides were identified in all tissue samples, and 756 proteins with more than 1.5-fold increase in abundance in IPMNs relative to NDs were identified, 45% of which were also identified in cyst fluids. The over-expression of selected proteins was validated by immunolabeling. Proteins and glycoproteins overexpressed in IPMNs included those involved in glycan biosynthesis and the immune system. In addition, multiomics clustering identified two subtypes of IPMNs. This study provides a foundation for understanding tumor progression and targets for earlier detection and therapies. SignificanceThis multilevel characterization of intraductal papillary neoplasms of the pancreas provides a foundation for understanding the changes in protein and glycoprotein expression during the progression from normal duct to intraductal papillary neoplasm, and to invasive pancreatic carcinoma, providing a foundation for informed approaches to earlier detection and treatment.

cancer biology↗

bioRxiv2021

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography - the synergistic combination of solid-state NMR, X-ray crystallography, and first-principles computational chemistry - holds remarkable promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in the enzyme active site - including hydrogen atom locations and tautomeric equilibria - it offers insight into structure, dynamics, and function. Here, we make use of this combined approach to characterize the -aminoacrylate intermediate in tryptophan synthase, a defining species for pyridoxal-5'-phosphate-dependent enzymes on the {beta}-elimination and replacement pathway. By uniquely identifying the protonation states of ionizable sites on the cofactor, substrates, and catalytic side chains, as well as the location and orientation of structural waters in the active site, a remarkably clear picture of structure and reactivity emerges. Most incredibly, this intermediate appears to be mere tenths of angstroms away from the preceding transition state in which the {beta}-hydroxyl of the serine substrate is lost. The position and orientation of the structural water immediately adjacent to the substrate {beta}-carbon suggests not only the fate of the hydroxyl group, but also the pathway back to the transition state and the identity of the active site acid-base catalytic residue. Reaction of this intermediate with benzimidazole (BZI), an isostere of the natural substrate, indole, shows BZI bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the BZI position, indole is positioned with C3 in contact with the -aminoacrylate C{beta} and aligned for nucleophilic attack. Significance StatementThe determination of active site protonation states is critical to gaining a full mechanistic understanding of enzymatic transformations; yet hydrogen positions are challenging to extract using the standard tools of structural biology. Here we make use of a joint solid-state NMR, X-ray crystallography, and first-principles computational approach that unlocks the investigation of enzyme catalytic mechanism at this fine level of chemical detail. For tryptophan synthase, this allows us to peer along the reaction coordinates into and out of the -aminoacrylate intermediate. Through this process, we are developing a high-resolution probe for structural biology that is keenly sensitive to proton positions - rivaling that of neutron diffraction, yet able to be applied under conditions of active catalysis to microcrystalline and non-crystalline materials.

biophysics↗