Biology subjects

Almeida, D.

Publications and source records attributed to Almeida, D..

14 recordsLinked to original sources

bioRxiv2026

Species demography, not metabolic rate, predicts community dominance independently of initial evenness

Understanding how species traits shape community properties is a central goal in ecology. But whether traits drive consistent patterns of dominance and assembly regardless of initial species abundances (evenness) remains unclear. We addressed this question using phytoplankton microcosm experiments to disentangle the effects of evenness and traits on community assembly and functioning, focusing on traits related to energy use (photosynthesis, size) alongside demographic parameters. Community assembly was highly deterministic, indicating that initial evenness had little influence on species dominance and final community structure. Instead, evenness drove community functioning. Demography was a stronger predictor of dominance than photosynthetic rates or individual size, suggesting that growth and competitive success depend on multiple metabolic processes that cannot be reduced to simpler proxies. These results show that community structure can emerge predictably across a range of initial conditions, and highlight the importance of demographic metrics over simpler metabolic descriptors for forecasting community outcomes.

ecology↗

bioRxiv2025

AVITI library prep miniaturization and combining with Illumina data for phylogenomic and population genomic analyses

Recent advancements in next generation sequencing approaches allow for expansion of evolutionary research into the discovery of genetic patterns and processes underlying diversification across scales. The increased popularity of the Element Bioscience AVITI platform, partially due to the high sequencing accuracy and low cost of reagents, is becoming a viable alternative approach for generating massive amounts of comparative sequencing data across diverse organismal lineages. Using a data set of five accessions from the monocot genus Costus, we tested miniaturization conditions for generating robust, cost-effective libraries and made comparisons of data generated by AVITI and Illumina sequencing platforms to investigate the potential for combining data for population genomic and phylogenomic analyses. Our results show that the AVITI and Illumina data sets are highly congruent in terms of inferring overlapping SNPs, with only a small fraction picked up by only one of the two platforms. The rates of duplication in miniaturized libraries were much higher than in full volume libraries and in the Illumina libraries, resulting in missing SNPs and less sequence coverage when volumes are reduced. For all generated libraries, most downstream evolutionary analyses, including clustering algorithms (such as PCA) and phylogenetic inference, yielded similar results. However, Structure analyses were less consistent across datasets, with data from the most miniaturized libraries being assigned to the wrong clusters. The AVITI platform should be seen as a cost-effective approach for generating genomic data for comparison across taxonomic lineages, even for ongoing projects where Illumina data already exists.

evolutionary biology↗

bioRxiv2024

Pervasive neurovascular dysfunction in the ventromedial prefrontal cortex of female depressed suicides with a history of childhood abuse

Exposure to early life adversity (ELA) poses a significant global public health concern, with profound pathophysiological implications for affected individuals. Studies suggest that ELA contributes to endothelial dysfunction, bringing into question the functional integrity of the neurovascular unit in brain regions vulnerable to chronic stress. Despite the importance of the neurovasculature in maintaining normal brain physiology, human neurovascular cells remain poorly characterized, particularly with regard to their contributory role in ELA-associated pathophysiologies. In this study, we present the first comprehensive transcriptomic analysis of intact microvessels isolated from postmortem ventromedial prefrontal cortex samples from adult healthy controls (CTRL) and matched depressed suicides with histories of ELA. Our findings point to substantive differences between men and women, with the latter exhibiting widespread gene expression changes at the neurovascular unit, including the key vascular nodal regulators KLF2 and KLF4, alongside a broad downregulation of immune-related pathways. These results suggest that the neurovascular unit plays a larger role in the neurobiological consequences of ELA in human females.

neuroscience↗

bioRxiv2024

Cortical networks responsive to phrase structure and subject island violations

In principle, functional neuroimaging provides uniquely informative data in addressing linguistic questions, because it can indicate distinct processes that are not apparent from behavioral data alone. This could involve adjudicating the source of unacceptability via the different patterns of elicited brain responses to different ungrammatical sentence types. However, it is difficult to interpret brain activations to syntactic violations. Such responses could reflect processes that have nothing intrinsically related to linguistic representations, such as domain-general executive function abilities. In order to facilitate the potential use of functional neuroimaging methods to identify the source of different syntactic violations, we conducted an fMRI experiment to identify the brain activation maps associated with two distinct syntactic violation types: phrase structure (created by inverting the order of two adjacent words within a sentence) and subject islands (created by extracting a wh-phrase out of an embedded subject). The comparison of these violations to control sentences surprisingly showed no indication of a generalized violation response, with almost completely divergent activation patterns. Phrase structure violations seemingly activated regions previously implicated in verbal working memory and structural complexity in sentence processing, whereas the subject islands appeared to activate regions previously implicated in conceptual-semantic processing, broadly defined. We review our findings in the context of previous research on syntactic and semantic violations using event- related potentials. Although our results suggest potentially distinct underlying mechanisms underlying phrase structure and subject island violations, our results are tentative and suggest important methodological considerations for future research in this area.

neuroscience↗

bioRxiv2024

Same Sentences, Different Grammars, Different Brain Responses: An MEG study on Case and Agreement Encoding in Hindi and Nepali Split-Ergative Structures

At first glance, the brains language network appears to be universal, but languages clearly differ. How does the brain adapt to the specific details of individual grammatical systems? Here, we present an MEG study on case and agreement in Hindi and Nepali. Both languages use split-ergative case systems. However, these systems interact with verb agreement differently - in Hindi, case features conspire to determine which noun phrase (NP) the verb agrees with (subject, object, or neither), but in Nepali the verb always agrees with the subject NP. We found that left inferior frontal and left anterior temporal regions are sensitive to case features in both languages. Across case configurations, these same brain areas in Hindi participants show different patterns of activity for sentences that require masculine vs. feminine marking on the verb, before the comprehenders encounter it. Additionally, the left temporoparietal junction in Hindi shows different activity for subject and object agreement configurations. Both findings are not observed in Nepali participants. We suggest that this brain response demonstrates a unique-to-Hindi selection of an agreement controller and pre-encoding of the verbs morphological features. This shows that brain activity reflects psycholinguistic processes that are intimately tied to grammatical features. HighlightsO_LIThe left inferior frontal lobe and the left anterior temporal lobe distinguish accusative objects versus bare object NPs in Hindi and Nepali, and pre-emptively encode gender agreement features in Hindi. C_LIO_LIThe left inferior parietal lobe shows a differential sensitivity to object-agreement and subject-agreement constructions in Hindi that is absent in Nepali C_LIO_LIMEG can reveal differences in neural activity that reflect specific requirements of different grammatical systems C_LI

neuroscience↗

bioRxiv2023

Universal method for the gentle isolation of intact microvessels from frozen tissue: a multiomic investigation into the neurovasculature

The neurovascular unit (NVU), comprised of endothelial cells, pericytes, smooth muscle cells, astrocytic endfeet and microglia together with neurons, is paramount for the proper function of the central nervous system. The NVU gatekeeps blood-brain barrier (BBB) properties which, as a system, experiences impairment in several neurological and psychiatric diseases, and contributes to pathogenesis. To better understand function and dysfunction at the NVU, isolation and characterization of the NVU is needed. Here, we describe a singular, standardized protocol to enrich and isolate microvessels from archived snap-frozen human and frozen mouse cerebral cortex using mechanical homogenization and centrifugation-separation that preserves the structural integrity and multicellular composition of microvessel fragments. For the first time, microvessels are isolated from postmortem vmPFC tissue and are comprehensively investigated using both RNA sequencing and Liquid Chromatography with tandem mass spectrometry (LC-MS-MS). Both the transcriptome and proteome are elucidated and compared, demonstrating that the isolated brain microvessel is a robust model for the NVU and can be used to generate highly informative datasets in both physiological and disease contexts.

neuroscience↗

bioRxiv2021

Impact of dose, duration and host immune status on ultrashort telacebec treatment in a mouse model of Buruli ulcer

Telacebec (Q203) is a new anti-tuberculosis drug in clinical development with extremely potent activity against Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU). The potency of Q203 has prompted investigation of its potential role in ultra-short, even single-dose, treatment regimens for BU in mouse models. However, the relationships of Q203 dose and duration and host immune status to treatment outcomes remain unclear, as does the risk of emergence of drug resistance with Q203 monotherapy. In the present study, immunocompetent BALB/c and immunocompromised SCID-beige mice were infected in both hind footpads and treated eight weeks later. In both mouse strains, controls received rifampin-clarithromycin; others received Q203 at 0.5 or 2 mg/kg/d for 5 or 10 days. Additionally, BALB/c mice received a single dose of 2.5 or 10 mg/kg or 3.3 mg/kg/d for 3 days. Treatment response was based on changes in footpad swelling and CFU counts at the end of treatment as well as 4 and 13 weeks after stopping treatment. Efficacy depended on total dose more than duration. Total doses of 5-20 mg/kg rendered nearly all BALB/c mice culture-negative 13 weeks post-treatment without selection of Q203-resistant bacteria. Although less potent in SCID-beige mice, Q203 still rendered the majority of footpads culture-negative at total doses of 10-20 mg/kg. However, Q203 resistance was identified in relapse isolates from some SCID-beige mice. Overall, these results support the potential of Q203 monotherapy for single-dose or other ultra-short therapy for BU, although highly immunocompromised hosts may require higher doses or durations and/or combination therapy.

microbiology↗

bioRxiv2021

Ultrashort treatment with telacebec alone and with companion drugs in immunocompetent and immunosuppressed mouse footpad models of Buruli ulcer

The antimicrobial treatment of Mycobacterium ulcerans infection, or Buruli ulcer (BU), has a long duration and is therefore burdensome and linked to indirect costs for affected patients. The new antimycobacterial drug telacebec (Q203) has previously shown promising treatment-shortening potential in mouse models of BU. In the present study, we investigated the potential of Q203 to reduce the treatment duration further. The first experiment investigated the possibility of cure by one, three or five doses of Q203 (2 mg/kg) with or without a companion drug (bedaquiline, BDQ, clofazimine, CFZ, or clarithromycin, CLR) in immunocompetent BALB/c mice. The second experiment assessed the effect of five doses of Q203 with or without BDQ or CFZ on Mycobacterium ulcerans infection of immunocompromised SCID-beige mice with the aim to evaluate the contribution of host immunity to treatment efficacy. In BALB/c mice, a treatment duration as short as 3 days was sufficient to prevent relapse in nearly all footpads and a single dose of Q203 with or without BDQ or CFZ prevented relapse in approximately 50% of footpads. Unlike in BALB/c mice, a small percentage of SCID-beige mouse footpads were culture-positive after a treatment duration of five days, highlighting an important role of host immunity for M. ulcerans clearance. Our results confirm the marked potency and prolonged bactericidal and sterilizing effects of Q203, even in immunocompromised SCID-beige mice.

microbiology↗

bioRxiv2020

Increased functional coupling of the mu opioid receptor in the anterior insula of depressed individuals

The mu opioid receptor (MOR) is a G protein-coupled receptor that plays an essential role in reward and hedonic processes, and that has been implicated in disorders such as depression and addiction. Over the last decade, several brain imaging studies in depressed patients have consistently found that dysregulation of MOR function occurs in particular in the anterior insular cortex, an important brain site for the perception of internal states and emotional regulation. To investigate molecular mechanisms that may underlie these effects, here we assessed genetic polymorphisms, expression, and functional G-protein coupling of MOR in a large post-mortem cohort (N=95) composed of depressed individuals who died by suicide, and healthy controls. Results indicated that depression, but not comorbid substance use disorder or acute opiate consumption, was associated with increased MOR activity. This effect was partly explained by a specific increase in expression of the inhibitory alpha G-protein subunit GNAI2. Consistent with previous neuroimaging studies, our findings support the notion that enhanced endogenous opioidergic tone in the anterior insula may buffer negative affective states in depressed individuals, a mechanism that could potentially contribute to the antidepressant efficacy of emerging opioid-based medications.

neuroscience↗

bioRxiv2020

Manipulation of a cation-{Pi} sandwich expands knowledge of the conformational flexibility of mammalian phenylalanine hydroxylase

Phenylalanine hydroxylase (PAH) is an allosteric enzyme responsible for maintaining phenylalanine (Phe) below neurotoxic levels; its failure results in phenylketonuria. Wild type (WT) PAH equilibrates among resting-state (RS-PAH) and activated (A-PAH) conformations, whose equilibrium position depends upon allosteric Phe binding to the A-PAH conformation. The RS-PAH conformation of WT rat PAH (rPAH) contains a cation-{pi} sandwich between Phe80, Arg123, and Arg420, which cannot exist in the A-PAH conformation. Phe80 variants F80A, F80D, F80L, and F80R were prepared; their conformational equilibrium was evaluated using native PAGE, size exclusion chromatography, ion exchange behavior, intrinsic protein fluorescence, enzyme kinetics, and limited proteolysis, each as a function of [Phe]. Like WT rPAH, F80A and F80D show allosteric activation by Phe while F80L and F80R are constitutively active. Maximal activity of all variants suggests relief of a rate-determining conformational change involving Phe80. Limited proteolysis of WT rPAH in the absence of Phe reveals facile cleavage within a C-terminal 4-helix bundle that is buried in the RS-PAH tetramer interface, reflecting dynamic dissociation of the RS-PAH conformation. This cleavage is not seen for the Phe80 variants, which all show proteolytic hypersensitivity in a linker that repositions during the RS-PAH to A-PAH conformational interchange. Hypersensitivity is corrected by addition of Phe such that all Phe80 variants become like WT rPAH and achieve the A-PAH conformation. Thus, manipulation of Phe80 perturbs the conformational space sampled by PAH, increasing the propensity to sample intermediates in the RS-PAH and A-PAH interchange, which are presumed on-pathway because they can readily achieve the A-PAH conformation by addition of Phe.

biochemistry↗

bioRxiv2020

Telacebec for ultra-short treatment of Buruli ulcer in a mouse model

Telacebec (Q203) is a new anti-tubercular drug with extremely potent activity against Mycobacterium ulcerans. Here, we explored the treatment-shortening potential of Q203 alone or in combination with rifampin (RIF) in a mouse footpad infection model. The first study compared Q203 at 5 and 10 mg/kg doses alone and with rifampin. Q203 alone rendered most mouse footpads culture-negative in 2 weeks. Combining Q203 with rifampin resulted in relapse-free cure 24 weeks after completing 2 weeks of treatment, compared to a 25% relapse rate in mice receiving RIF+clarithromycin, the current standard of care, for 4 weeks. The second study explored the dose-ranging activity of Q203 alone and with RIF, including the extended activity of Q203 after treatment discontinuation. The bactericidal activity of Q203 persisted for [≥] 4 weeks beyond the last dose. All mice receiving just 1 week of Q203 at 2-10 mg/kg were culture-negative 4 weeks after stopping treatment. Mice receiving 2 weeks of Q203 at 0.5, 2 and 10 mg/kg were culture-negative 4 weeks after treatment. RIF did not increase the efficacy of Q203. A pharmacokinetics sub-study revealed that Q203 doses of 2-10 mg/kg in mice produce plasma concentrations similar to those produced by 100-300 mg doses in humans, with no adverse effect of RIF on Q203 concentrations. These results indicate the extraordinary potential of Q203 to reduce the duration of treatment necessary for cure to [≤] 1 week (or 5 doses of 2-10 mg/kg) in our mouse footpad infection model and warrant further evaluation of Q203 in clinical trials.

microbiology↗

bioRxiv2019

Contribution of pretomanid to novel regimens containing bedaquiline with either linezolid or moxifloxacin and pyrazinamide in murine models of tuberculosis

Novel regimens combining bedaquiline and pretomanid with either linezolid (BPaL regimen) or moxifloxacin and pyrazinamide (BPaMZ regimen) shorten the treatment duration needed to cure TB in BALB/c mice compared to the first-line regimen and have yielded promising results in initial clinical trials. However, the independent contribution of the investigational new drug pretomanid to the efficacy of BPaMZ has not been examined and its contribution to BPaL has been examined only over the first 2 months of treatment. In the present study, the addition of pretomanid to BL increased bactericidal activity, prevented emergence of bedaquiline resistance, and shortened the duration needed to prevent relapse with drug-susceptible isolates by at least 2 months in BALB/c mice. Addition of pretomanid to BMZ resulted in a 1 log10 greater CFU reduction after 1 month of treatment and/or reduced the number of mice relapsing in each of 2 experiments in BALB/c mice and in immunocompromised nude mice. Bedaquiline-resistant isolates were found at relapse in only one BMZ-treated nude mouse. Treatment of infection with a pyrazinamide-resistant mutant in BALB/c mice with BPaMZ prevented selection of bedaquiline-resistant mutants and reduced the proportion of mice relapsing compared to BMZ alone. Among severely ill C3HeB/FeJ mice with caseous pneumonia and cavitation, BPaMZ increased median survival ([≥]60 vs. 21 days) and reduced median lung CFU by 2.4 log10 at 1 month compared to BMZ. In conclusion, in 3 different mouse models, pretomanid contributed significantly to the efficacy of the BPaMZ and BPaL regimens, including restricting the selection of bedaquiline-resistant mutants.

pharmacology and toxicology↗

bioRxiv2018

CD44v6 expression is a novel predictive marker of therapy response and poor prognosis in gastric cancer patients

Late diagnosis, modest treatment options and lack of predictive markers of therapy response dictate the poor overall survival (OS) of [~]1 year in most gastric cancer (GC) patients. We hypothesized that the level of CD44v6 expression in tumor cells could predict therapy response and prognosis in GC patients.\n\nWe analyzed a surgical tumor series of GC patients for the extension of CD44v6 membranous immuno-expression, clinical-pathological features, patient survival, and response to therapy. By integrating this information, we assessed the value of CD44v6 expression to predict benefit from current treatment regimens and prognosis in GC patients. We used GC cell lines and mouse xenografts to assess and/validate the biological impact of CD44v6 expression in GC cells behavior.\n\nWe demonstrated that GC patients whose tumors present higher levels of CD44v6 membranous expression benefit from adding chemotherapy to surgery as opposed to those without CD44v6 expression. Moreover, patients bearing CD44_high tumors presented worse OS than those bearing CD44_absent/low tumors, consolidating the role of CD44v6 expression as an independent factor of poor prognosis in this disease. Finally, our in vitro and patients data pinpoints the CD44v6+ cell population as the driver of tumor recurrence following conventional chemotherapy, in heterogeneous tumors composed by CD44v6- and CD44v6+ cells.\n\nOur study pioneers the identification of CD44v6 as a potential predictive marker of response to conventional chemotherapy, and consolidates CD44v6 as an independent marker of poor prognosis in GC. Overall, our data strongly supports selection of patients with high CD44v6 expressing tumors for conventional chemotherapy with or without surgery, regardless of the TNM stage.

cancer biology↗

bioRxiv2018

High-dose rifamycins enable shorter oral treatment in a murine model of Mycobacterium ulcerans disease

Buruli ulcer (BU), caused by Mycobacterium ulcerans, is a neglected tropical skin and soft tissue infection that is associated with disability and social stigma. The mainstay of BU treatment is an eight-week course of 10 mg/kg rifampin (RIF) and 150 mg/kg streptomycin (STR). Recently, the injectable STR has been shown to be replaceable with oral clarithromycin (CLR) for smaller lesions for the last four weeks of treatment. A shorter, all-oral, highly efficient regimen for BU is needed, as the long treatment duration and indirect costs currently burden patients and health systems. Increasing the dose of RIF or replacing it with the more potent rifamycin drug rifapentine (RPT) could provide such a regimen. Here, we performed a dose-ranging experiment of RIF and RPT in combination with CLR over four weeks of treatment in a mouse model of M. ulcerans disease. A clear dose-dependent effect of RIF on both clinical and microbiological outcomes was found, with no ceiling effect observed with tested doses up to 40 mg/kg. RPT-containing regimens were more effective on M. ulcerans. All RPT-containing regimens achieved culture negativity after only four weeks while only the regimen with the highest RIF dose (40 mg/kg) did so. We conclude that there is dose-dependent efficacy of both RIF and RPT and that a ceiling effect is not reached with the current standard regimen used in the clinic. A regimen based on higher rifamycin doses that are currently being evaluated against tuberculosis in clinical trials could shorten and improve therapy of Buruli ulcer.

microbiology↗