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1.
Artículo en Inglés | MEDLINE | ID: mdl-39303293

RESUMEN

This study investigated the impact of menstrual cycle (MC) phases and resistance training (RT) on muscle cross-sectional area (CSA) in two MCs utilizing a within-subject design. Twenty women with regular MCs had their legs randomly allocated to either the control (CON) or RT condition, which included 16 training sessions over two MCs. CSA, estradiol (E2), and progesterone (P4) were assessed during the menstruation (M), ovulation (O), and luteal (L) phases in the first (M1, O1, L1) and second (M2, O2, L2) MCs and at the beginning of the third MC (M3). P4 values were significantly higher during the luteal phase than during menstruation (P < 0.0001) and ovulation (P < 0.0001). No significant differences in E2 concentrations were observed between the MC phases (P = 0.08). For the RT condition, the CSA showed significant increases at O2, L2, and M3 compared to baseline (M1) (all P < 0.0001). No significant changes were observed for the CON condition during the two MCs (P > 0.05). However, RT condition showed a significant change in average CSA across two MCs. Additionally, individual analyses revealed that 19 participants showed variation in CSA above or below the minimum detectable difference during the two MCs. These findings suggest that changes in muscle CSA observed during two MCs may not be exclusively attributed to RT.

2.
Artículo en Inglés | MEDLINE | ID: mdl-39231109

RESUMEN

This case report describes a new type of perifoveal retinal vascular abnormality (RVA) incidentally discovered during a posterior vitreous detachment (PVD) investigation. A 65-year-old woman with sudden central visual loss displayed a unilateral focal telangiectatic venule in the perifoveal area. Multimodal imaging documented the vascular abnormality and associated retinal changes. Despite symptom resolution, the RVA persisted. This case represents a unique presentation of perifoveal RVA, likely an atypical form of macular telangiectasia. The sequential imaging documentation during a process of PVD with central bouquet traction provides insights into the underlying mechanisms in addition to diagnosing and monitoring perifoveal RVAs. [Ophthalmic Surg Lasers Imaging Retina 2024;55:XX-XX.].

3.
Nat Commun ; 15(1): 6839, 2024 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-39122697

RESUMEN

There has been a dramatic increase in the identification of non-canonical translation and a significant expansion of the protein-coding genome. Among the strategies used to identify unannotated small Open Reading Frames (smORFs) that encode microproteins, Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple genomic sites are removed since they cannot be unambiguously assigned to a specific genomic location. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of multi-mapping alignments, such that smORFs residing in these regions cannot be identified by Ribo-Seq. Moreover, it has been challenging to identify protein evidence for Ribo-Seq. To solve this, we developed Rp3, a pipeline that integrates proteogenomics and Ribosome profiling to provide unambiguous evidence for a subset of microproteins missed by current Ribo-Seq pipelines. Here, we show that Rp3 maximizes proteomics detection and confidence of microprotein-encoding smORFs.


Asunto(s)
Sistemas de Lectura Abierta , Proteogenómica , Ribosomas , Ribosomas/metabolismo , Ribosomas/genética , Proteogenómica/métodos , Sistemas de Lectura Abierta/genética , Biosíntesis de Proteínas , Humanos , Proteómica/métodos , Proteínas/genética , Proteínas/metabolismo , Perfilado de Ribosomas
4.
Methods Mol Biol ; 2836: 19-34, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38995533

RESUMEN

Genome annotation has historically ignored small open reading frames (smORFs), which encode a class of proteins shorter than 100 amino acids, collectively referred to as microproteins. This cutoff was established to avoid thousands of false positives due to limitations of pure genomics pipelines. Proteogenomics, a computational approach that combines genomics, transcriptomics, and proteomics, makes it possible to accurately identify these short sequences by overlaying different levels of omics evidence. In this chapter, we showcase the use of µProteInS, a bioinformatics pipeline developed for the identification of unannotated microproteins encoded by smORFs in bacteria. The workflow covers all the steps from quality control and transcriptome assembly to the scoring and post-processing of mass spectrometry data. Additionally, we provide an example on how to apply the pipeline's machine learning method to identify high-confidence spectra and pinpoint the most reliable identifications from large datasets.


Asunto(s)
Proteínas Bacterianas , Biología Computacional , Sistemas de Lectura Abierta , Proteogenómica , Flujo de Trabajo , Sistemas de Lectura Abierta/genética , Proteogenómica/métodos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biología Computacional/métodos , Proteómica/métodos , Aprendizaje Automático , Bacterias/genética , Bacterias/metabolismo , Programas Informáticos , Espectrometría de Masas/métodos , Micropéptidos
5.
J Glaucoma ; 2024 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-39018052

RESUMEN

PRCIS: Selective laser trabeculoplasty (SLT) and medical therapy groups displayed comparable intraocular pressure (IOP) at most follow-ups. SLT was associated with significantly decreased rates of glaucoma surgeries, antiglaucomatous medications, and ocular adverse effects. PURPOSE: To evaluate the efficacy and safety of selective laser trabeculoplasty (SLT) compared to medical therapy in the treatment of open-angle glaucoma (OAG) or ocular hypertension (OHT). METHODS: A systematic search was performed in PubMed, Embase, Cochrane Library and Web of Science databases. Randomized controlled trials (RCTs) comparing SLT with medical therapy were included. We computed mean differences (MDs) or standardized mean differences (STDs) for continuous endpoints and risk ratios (RRs) for binary endpoints, with 95% confidence intervals (CIs). Heterogeneity was assessed with I2 statistics. Software R, version 4.2.1, was used for statistical analyses. Subgroup analyses were performed on treatment-naive patients and on the class of drugs in the medical therapy group. RESULTS: Fourteen RCTs comprising 1,706 patients were included, of whom 936 were submitted to SLT. Medical therapy was associated with a significantly improved IOP at 1 month and a higher proportion of patients achieving ≥20% IOP reduction. There were no significant differences between groups in IOP at 2, 3, 6, and 12 months, IOP fluctuation, rate of eyes at target IOP, visual field, and quality of life. The SLT group exhibited significantly decreased rates of glaucoma surgeries, antiglaucoma medications, and ocular adverse effects. CONCLUSION: SLT demonstrated comparable efficacy to medical therapy in IOP control at most follow-ups, along with favorable impacts on critical treatment-related factors. Our findings support SLT as a safe and effective treatment for OAG or OHT.

6.
Anim Reprod ; 21(2): e20230131, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38912163

RESUMEN

In reproductive technologies, uncovering the molecular aspects of oocyte and embryo competence under different conditions is crucial for refining protocols and enhancing efficiency. RNA-seq generates high-throughput data and provides transcriptomes that can undergo additional computational analyses. This study presented the transcriptomic profiles of in vitro matured oocytes and blastocysts produced in vitro from buffalo crossbred (Bubalus bubalis), coupled with gene co-expression and module preservation analysis. Cumulus Oophorus Complexes, obtained from slaughterhouse-derived ovaries, were subjected to in vitro maturation to yield metaphase II oocytes (616) or followed in vitro fertilization and culture to yield blastocysts for sequencing (526). Oocyte maturation (72%, ±3.34 sd) and embryo development (21.3%, ±4.18 sd) rates were obtained from three in vitro embryo production routines following standard protocols. Sequencing of 410 metaphase II oocytes and 70 hatched blastocysts (grade 1 and 2) identified a total of 13,976 genes, with 62% being ubiquitously expressed (8,649). Among them, the differentially expressed genes (4,153) and the strongly variable genes with the higher expression (fold-change above 11) were highlighted in oocytes (BMP15, UCHL1, WEE1, NLRPs, KPNA7, ZP2, and ZP4) and blastocysts (APOA1, KRT18, ANXA2, S100A14, SLC34A2, PRSS8 and ANXA2) as representative indicators of molecular quality. Additionally, genes exclusively found in oocytes (224) and blastocysts (2,200) with specific biological functions were identified. Gene co-expression network and module preservation analysis revealed strong preservation of functional modules related to exosome components, steroid metabolism, cell proliferation, and morphogenesis. However, cell cycle and amino acid transport modules exhibited weak preservation, which may reflect differences in embryo development kinetics and the activation of cell signaling pathways between buffalo and bovine. This comprehensive transcriptomic profile serves as a valuable resource for assessing the molecular quality of buffalo oocytes and embryos in future in vitro embryo production assays.

7.
Int J Sports Med ; 45(9): 690-697, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38729165

RESUMEN

This study investigated the effects of different resistance training (RT) volumes quantified by weekly sets at high intensity (load and effort) on dynamic strength adaptations and psychophysiological responses in trained individuals. Twenty-four athletes were randomly allocated to three groups that performed three (3 S, n=8), six (6 S, n=8), and nine (9 S, n=8) weekly sets, respectively, three times a week on the barbell back squat and bench press during an 8-week period. While all groups showcased strength gains (p<0.05), post hoc comparisons revealed that 6 S and 9 S elicited greater strength adaptations than 3 S in barbell back squat (p=0.027 and p=0.004, respectively) and bench press (p=0.001 and p=0.044, respectively). There were no differences between 6 S and 9 S conditions for back squat (p=0.999) and bench press (p=0.378). Although a time effect was observed for Session-RPE (p=0.014) and Total Quality Recovery scale (p=0.020), psychophysiological responses were similar among groups. Our findings suggest that performing six and nine weekly sets at high intensities led to greater strength gains compared to three weekly sets in strength-trained individuals, despite similar psychophysiological responses.


Asunto(s)
Adaptación Fisiológica , Fuerza Muscular , Entrenamiento de Fuerza , Humanos , Fuerza Muscular/fisiología , Entrenamiento de Fuerza/métodos , Masculino , Adulto Joven , Percepción/fisiología , Atletas , Levantamiento de Peso/fisiología , Adulto , Esfuerzo Físico/fisiología , Femenino
8.
J Mol Biol ; 436(10): 168559, 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38580077

RESUMEN

Upstream open reading frames (uORFs) are cis-acting elements that can dynamically regulate the translation of downstream ORFs by suppressing downstream translation under basal conditions and, in some cases, increasing downstream translation under stress conditions. Computational and empirical methods have identified uORFs in the 5'-UTRs of approximately half of all mouse and human transcripts, making uORFs one of the largest regulatory elements known. Because the prevailing dogma was that eukaryotic mRNAs produce a single functional protein, the peptides and small proteins, or microproteins, encoded by uORFs were rarely studied. We hypothesized that a uORF in the SLC35A4 mRNA is producing a functional microprotein (SLC35A4-MP) because of its conserved amino acid sequence. Through a series of biochemical and cellular experiments, we find that the 103-amino acid SLC35A4-MP is a single-pass transmembrane inner mitochondrial membrane (IMM) microprotein. The IMM contains the protein machinery crucial for cellular respiration and ATP generation, and loss of function studies with SLC35A4-MP significantly diminish maximal cellular respiration, indicating a vital role for this microprotein in cellular metabolism. The findings add SLC35A4-MP to the growing list of functional microproteins and, more generally, indicate that uORFs that encode conserved microproteins are an untapped reservoir of functional microproteins.


Asunto(s)
Membranas Mitocondriales , Proteínas Mitocondriales , Proteínas de Transporte de Nucleótidos , Sistemas de Lectura Abierta , Humanos , Regiones no Traducidas 5'/genética , Secuencia de Aminoácidos , Mitocondrias/metabolismo , Mitocondrias/genética , Membranas Mitocondriales/metabolismo , Proteínas Mitocondriales/metabolismo , Proteínas Mitocondriales/genética , Sistemas de Lectura Abierta/genética , Biosíntesis de Proteínas , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas de Transporte de Nucleótidos/genética , Proteínas de Transporte de Nucleótidos/metabolismo , Células HEK293
9.
Anim Reprod ; 21(1): e20230107, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38562606

RESUMEN

One of the crucial aspects to be considered for successful in vitro production (IVP) of embryos is the composition of the various media used throughout the stages of this reproductive biotechnology. The cell culture media employed should fulfill the metabolic requirements of both gametes during oocyte maturation and sperm development, as well as the embryo during its initial cell divisions. Most IVP protocols incorporate blood serum into the media composition as a source of hormones, proteins, growth factors, and nutrients. Numerous studies have suggested Platelet-Rich Plasma (PRP) as a substitute for fetal sera in cell culture, particularly for stem cells. Therefore, the objective of this study is to assess the potential use of PRP as a replacement for fetal bovine serum (FBS) during oocyte maturation for in vitro production of bovine embryos. During in vitro maturation (IVM), cumulus-oocyte complexes (COCs) were allocated into the following experimental groups: Group G1 (IVM medium with 5% PRP); Group G2 (MIV medium with 5% PRP and 5% SFB); Group G3 (MIV medium with 5% SFB); and Group G4 (MIV medium without either PRP or SFB). Subsequently, the cumulus-oocyte complexes were fertilized with semen from a single bull, and the resulting zygotes were cultured for seven days. Cleavage and blastocyst formation rates were assessed on days 2 and 7 of embryonic development, respectively. The quality of matured COCs was also evaluated by analyzing the gene expression of HSP70, an important protein associated with cellular stress. The results demonstrated that there were no significant differences among the experimental groups in terms of embryo production rates, both in the initial cleavage stages and blastocyst formation (except for the G4 group, which exhibited a lower blastocyst formation rate on D7, as expected). This indicates that PRP could be a cost-effective alternative to SFB in the IVP of embryos.

10.
Reprod Domest Anim ; 59(3): e14548, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38459830

RESUMEN

The in vivo fertilization process occurs in the presence of follicular fluid (FF). The aim of this study was to evaluate the effect of in vitro fertilization medium supplementation with 5% or 10% bovine follicular fluid (BFF) on the production of in vitro bovine embryos. FF was collected from ovarian follicles with a diameter of 8-10 mm, and cumulus-oocyte complexes (COCs) were co-incubated with sperm for 24 h in the commercial medium BotuFIV® (BotuPharma©), being distributed among the experimental groups: oocytes fertilized in a control medium; oocytes fertilized in a medium supplemented with 5% BFF; and oocytes fertilized in a medium supplemented with 10% BFF. After fertilization, the zygotes were cultured in vitro for 8 days. Embryo development was assessed through cleavage rates (day 2) and blastocyst formation rates (day 8). The relative expression of the genes OCT4, IFNT2, BAX, HSP70 and SOD2 was measured using the real-time polymerase chain reaction method. There was no difference (p > .05) among the different experimental groups in terms of cleavage rates and blastocyst formation rates. Regarding the gene expression results, only the blastocysts from oocytes fertilized with 10% BFF showed significantly lower expression of IFNT2 (p = .003) and SOD2 (p = .01) genes compared to blastocysts from oocytes fertilized in control medium alone, while there was no difference between blastocyst from oocytes fertilized in control medium and the ones from oocytes fertilized with 5% BFF. In addition to this, the blastocysts from oocytes fertilized with 5% BFF showed significantly reduced levels of expression of the heat shock protein HSP70 (p < .001) and the pro-apoptotic protein BAX (p = .015) compared to blastocysts from oocytes fertilized with control medium. This may indicate that lower supplementation of BFF to the IVF medium creates a more suitable environment for fertilization and is less stressful for the zygote.


Asunto(s)
Fertilización In Vitro , Líquido Folicular , Femenino , Masculino , Bovinos , Animales , Proteína X Asociada a bcl-2/genética , Proteína X Asociada a bcl-2/metabolismo , Fertilización In Vitro/veterinaria , Semen , Oocitos , Desarrollo Embrionario , Blastocisto/metabolismo , Proteínas HSP70 de Choque Térmico/genética , Fertilización
11.
Environ Sci Pollut Res Int ; 31(19): 28025-28039, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38523211

RESUMEN

Azo dyes, widely used in the textile industry, contribute to effluents with significant organic content. Therefore, the aim of this work was to synthesize cobalt ferrite (CoFe2O4) using the combustion method and assess its efficacy in degrading the azo dye Direct Red 80 (DR80). TEM showed a spherical structure with an average size of 33 ± 12 nm. Selected area electron diffraction and XRD confirmed the presence of characteristic crystalline planes specific to CoFe2O4. The amount of Co and Fe metals were determined by ICP-OES, indicating an n(Fe)/n(Co) ratio of 2.02. FTIR exhibited distinct bands corresponding to Co-O (455 cm-1) and Fe-O (523 cm-1) bonds. Raman spectroscopy detected peaks associated with octahedral and tetrahedral sites. For the first time, the material was applied to degrade DR80 in an aqueous system, with the addition of persulfate. Consistently, within 60 min, these trials achieved nearly 100% removal of DR80, even after the material had undergone five cycles of reuse. The pseudo-second-order model was found to be the most fitting model for the experimental data (k2 = 0.07007 L mg-1 min-1). The results strongly suggest that degradation primarily occurred via superoxide radicals and singlet oxygen. Furthermore, the presence of UV light considerably accelerated the degradation process (k2 = 1.54093 L mg-1 min-1). The material was applied in a synthetic effluent containing various ions, and its performance consistently approached 100% in the photo-Fenton system. Finally, two degradation byproducts were identified through HPLC-MS/MS analysis.


Asunto(s)
Cobalto , Compuestos Férricos , Oxígeno Singlete , Cobalto/química , Compuestos Férricos/química , Oxígeno Singlete/química , Superóxidos/química , Compuestos Azo/química , Contaminantes Químicos del Agua/química , Colorantes/química , Hierro/química , Peróxido de Hidrógeno/química
12.
Artículo en Inglés | MEDLINE | ID: mdl-38471086

RESUMEN

PURPOSE: To describe two cases of concentric macular rings (CMR) sign in patients with combined hamartoma of retina and retinal pigment epithelium (CHRRPE). METHODS: History and clinical examination, spectral-domain optical coherence tomography (SD-OCT), and optic coherence tomography angiography (OCTA). RESULTS: The first patient was a 26-year-old woman with clinical diagnosis of Neurofibromatosis type 2. The Best-Corrected Visual Acuity (BCVA) was 20/25 in the right eye (OD) and 20/20 in the left eye (OS). She presented a subtle grayish lesion in the macular region of OD. On macular SD-OCT, there was a thickened and disorganized retina, suggestive of CHRRPE. In addition, at the parafoveal region, there was a dentate pattern in the outer plexiform layer (OPL) and Henle fiber layer (HFL) on cross-sectional SD-OCT. OCTA showed no foveal avascular zone (FAZ) in OD and Optos ultra-wide-field revealed CMR sign in this eye. The second patient was a 14-year-old boy, with diabetes mellitus type 1. His BCVA was 20/25 in OD and 20/20 in OS. He had a subtle whitish lesion in the macular region of OD, with SD-OCT findings suggestive of CHRRPE. Similar to the first case, there was a dentate pattern in the OPL and HFL, on SD-OCT. In OD, blue reflectance images exhibited the CMR sign, and OCTA showed absent FAZ. CONCLUSION: CHRRPE may be related to changes in the OPL and HFL interface and may present the CMR sign.

13.
Eur J Ophthalmol ; 34(2): NP68-NP72, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-37671424

RESUMEN

PURPOSE: To report a case of exudative perifoveal exudative vascular anomalous complex (ePVAC) in a Brazilian healthy patient that underwent a complete resolution after aflibercept intravitreal injections. CASE DESCRIPTION: A 41-year-old healthy Brazilian man complained of acute central vision loss in his right eye (RE). Fundus examination showed a perifoveal hemorrhagic aneurysmal lesion, accompanied by several hard exudates in RE. On fluorescein angiography, these abnormalities showed a progressive hyperfluorescence with surrounding leakage. Optical coherence tomography (OCT) revealed a deep, perifoveal hyporeflective cystic space with a hyperreflective wall and hyperreflective material inside of fibrin-like aspect. Around this aneurism, intraretinal hyporeflective spaces suggestive of exudation were detected. Nor pathological flow signal, or telangiectatic dilations were evidenced on OCT-angiography. Therefore, a diagnosis of exudative ePVAC in RE was hypothesized. After an initial observation, the patient underwent three monthly aflibercept intravitreal injections (0.05 ml/2 mg), with a significative anatomical and functional improvement after two weeks from first dose. On last follow-up at five months from baseline, patient experienced no evidence of new exudation and a stable visual acuity. DISCUSSION: Placental growth factor (PlGF) may impact on pericytes' dropout, and thus on ePVAC development. In contrast to the other anti-VEGF drugs, aflibercept is the only molecule contrasting PlGF. Therefore, aflibercept would act on ePVAC not as an anti-VEGF drug, but rather as an anti-PlGF one. CONCLUSION: This report encouraged the use of aflibercept as a therapeutic option for ePVAC. Further studies are required to confirm our result and the impact of PlGF on ePVAC pathogenesis.


Asunto(s)
Receptores de Factores de Crecimiento Endotelial Vascular , Malformaciones Vasculares , Masculino , Humanos , Femenino , Adulto , Inyecciones Intravítreas , Brasil , Factor de Crecimiento Placentario/uso terapéutico , Receptores de Factores de Crecimiento Endotelial Vascular/uso terapéutico , Proteínas Recombinantes de Fusión/uso terapéutico , Angiografía con Fluoresceína/métodos , Malformaciones Vasculares/diagnóstico , Malformaciones Vasculares/tratamiento farmacológico , Tomografía de Coherencia Óptica/métodos , Inhibidores de la Angiogénesis/uso terapéutico
14.
Med Sci Sports Exerc ; 56(3): 553-563, 2024 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-37796222

RESUMEN

PURPOSE: This study investigated the effect of progressively adding sets for the lower limb every 2 wk versus performing a constant set volume in resistance-trained males. METHODS: Thirty-one resistance-trained males (age = 24.4 ± 2.9 yr, height = 175.5 ± 6.5 cm, body mass = 80.1 ± 9.4 kg, body fat = 14.4% ± 3.1%, resistance training [RT] experience = 5.1 ± 2.2 yr; one-repetition maximum [1RM] barbell back squat: body mass ratio = 1.7 ± 0.1 a.u.) were randomly allocated into a constant group (CG, n = 10), a four-set progression group (4SG, n = 10) or a six-set progression group (6SG, n = 11). After a 2-wk washout period and another 2-wk familiarization period, participants performed a lower-limb training program twice a week for 12 wk. Maximum dynamic strength (1RM) in the barbell back squat, vastus lateralis cross-sectional area, and the sum of lateral thigh muscle thickness at 30%, 50%, and 70% of the femur length were assessed at baseline and after the 12-wk training program. RESULTS: Regarding 1RM, multiple comparisons revealed that 6SG elicited higher muscle strength gains than 4SG ( P = 0.002) and CG ( P < 0.0001), and 4SG had greater improvements than CG ( P = 0.023). Cross-sectional area and sum of lateral thigh muscle thickness showed no between-group differences ( P = 0.067 and P = 0.076, respectively). However, an inspection of 95% confidence intervals suggests a potential dose-response relationship, with results appearing to plateau in the higher volume conditions. CONCLUSIONS: Our results suggest that progressively adding four or six sets per week every 2 wk elicited greater lower-limb strength in resistance-trained individuals over a 12-wk training period. Although our findings indicate a possible small benefit for higher volume conditions regarding hypertrophic adaptations in this population, the limited certainty of our findings warrants caution.


Asunto(s)
Músculo Esquelético , Entrenamiento de Fuerza , Masculino , Humanos , Adulto Joven , Adulto , Músculo Esquelético/fisiología , Músculo Cuádriceps , Hipertrofia , Muslo , Fuerza Muscular/fisiología , Entrenamiento de Fuerza/métodos
15.
bioRxiv ; 2023 Oct 02.
Artículo en Inglés | MEDLINE | ID: mdl-37808637

RESUMEN

There has been a dramatic increase in the identification of non-conical translation and a significant expansion of the protein-coding genome and proteome. Among the strategies used to identify novel small ORFs (smORFs), Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple sites in the genome are computationally removed since they cannot unambiguously be assigned to a specific genomic location, or to a specific transcript in the case of multiple isoforms. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of ambiguous and multi-mapping alignments, such that smORFs that reside in these regions cannot be identified by Ribo-Seq. Here, we show that the inclusion of proteogenomics to create a Ribosome Profiling and Proteogenomics Pipeline (RP3) bypasses this limitation to identify a group of microprotein-encoding smORFs that are missed by current Ribo-Seq pipelines. Moreover, we show that the microproteins identified by RP3 have different sequence compositions from the ones identified by Ribo-Seq-only pipelines, which can affect proteomics identification. In aggregate, the development of RP3 maximizes the detection and confidence of protein-encoding smORFs and microproteins.

16.
MethodsX ; 11: 102419, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37885760

RESUMEN

Currently, Brazil is one of the world's largest grain producers and exporters. Agriculture has already entered its 4.0 version (2017), also known as digital agriculture, when the industry has entered the 4.0 era (2011). This new paradigm uses Internet of Things (IoT) techniques, sensors installed in the field, network of interconnected sensors in the plot, drones for crop monitoring, multispectral cameras, storage and processing of data in Cloud Computing, and Big Data techniques to process the large volumes of generated data. One of the practical options for implementing precision agriculture is the segmentation of the plot into management zones, aiming at maximizing profits according to the productive potential of each zone, being economically viable even for small producers. Considering that climate factors directly influence yield, this study describes the development of a sensor network for climate monitoring of management zones (microclimates), allowing the identification of climate factors that influence yield at each of its stages.•Application of the internet of things to assist in decision making in the agricultural production system.•AgDataBox (ADB-IoT) web platform has an Application Programming Interface (API).•An agrometeorological station capable of monitoring all meteorological parameters was developed (Kate 3.0).

17.
Int J Retina Vitreous ; 9(1): 53, 2023 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-37658442

RESUMEN

BACKGROUND: First described by Gaucher and associates in 2008, dome-shaped macula (DSM) is an anterior convex protrusion of the macula visible on OCT (optical coherence tomography). Visual impairment in DSM results mainly from sub-foveal serous retinal detachment (SRD). Herein, this original study from retrospective data analysis evaluate the anatomical and functional effects of Pascal® short-pulse (SP) laser plus endpoint management (EpM) subthreshold diffuse laser (SDL) in patients with SRD due to DSM. METHODS: This retrospective study included seven consecutive patients (eight eyes) with SRD secondary to dome-shaped macula who underwent a comprehensive ophthalmological evaluation including logMAR BCVA, slit-lamp biomicroscopy, indirect ophthalmoscopy, and spectral-domain optical coherence tomography (SD-OCT) (Spectralis; Heidelberg Engineering, Germany) before combined Pascal® SP laser plus EpM-SDL with 1 to 6 month intervals, postoperatively, with a mean ± standard error (SE) follow-up time of 12.92 ± 1.34 months. RESULTS: Eight eyes from seven patients were analyzed in this study. At baseline, mean BCVA (LogMAR) ± standard error (SE) and mean CST (central subfield thickness)(µm) ± SE were 0.6125 ± 0.14 and 412.50 ± 24.65, respectively. After a mean follow-up time of 12.92 ± 1.34 months, mean CST (µm) ± SE and BCVA (LogMAR) ± SE were 294.75 ± 19.68 (p = 0.0078) and 0.4537 ± 0.12 (p = 0.0313), respectively. A statistically significant reduction in mean CST and an improvement in mean BCVA were noted after SRD resolution with laser therapy application. The mean serous retinal detachment resolution time (months) ± SE was 3.75 ± 1.08. No adverse events were registered, including enlargement of atrophic alterations and choroidal neovascularization. CONCLUSIONS: The novel combined laser modality with Pascal® SP laser plus EpM-SDL treatment may induce subretinal fluid regression and BCVA improvement 1 year after treatment in DSM patients with SRD.

18.
Tissue Cell ; 83: 102157, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37451011

RESUMEN

Cysteine proteases orchestrate bone remodeling, and are inhibited by cystatins. In reinforcing our hypothesis that exogenous and naturally obtained inhibitors of cysteine proteases (cystatins) act on bone remodeling, we decided to challenge osteoblasts with sugarcane-derived cystatin (CaneCPI-5) for up to 7 days. To this end, we investigated molecular issues related to the decisive, preliminary stages of osteoblast biology, such as adhesion, migration, proliferation, and differentiation. Our data showed that CaneCPI-5 negatively modulates both cofilin phosphorylation at Ser03, and the increase in cytoskeleton remodeling during the adhesion mechanism, possibly as a prerequisite to controlling cell proliferation and migration. This is mainly because CaneCPI-5 also caused the overexpression of the CDK2 gene, and greater migration of osteoblasts. Extracellular matrix remodeling was also evaluated in this study by investigating matrix metalloproteinase (MMP) activities. Our data showed that CaneCPI-5 overstimulates both MMP-2 and MMP-9 activities, and suggested that this cellular event could be related to osteoblast differentiation. Additionally, differentiation mechanisms were better evaluated by investigating Osterix and alkaline phosphatase (ALP) genes, and bone morphogenetic protein (BMP) signaling members. Altogether, our data showed that CaneCPI-5 can trigger biological mechanisms related to osteoblast differentiation, and broaden the perspectives for better exploring biotechnological approaches for bone disorders.


Asunto(s)
Cistatinas , Proteasas de Cisteína , Saccharum , Osteogénesis/genética , Saccharum/genética , Diferenciación Celular/genética , Cistatinas/genética , Cistatinas/farmacología , Cistatinas/metabolismo , Factores de Transcripción/metabolismo , Proteasas de Cisteína/metabolismo , Osteoblastos , Proteína Morfogenética Ósea 2/metabolismo
19.
Drug Chem Toxicol ; : 1-7, 2023 Jun 08.
Artículo en Inglés | MEDLINE | ID: mdl-37288763

RESUMEN

Despite the cytotoxicity and embryotoxicity previously reported artesunate is a recommended drug to treat malaria for adults, children, and women in the first trimester of pregnancy. To address the putative effects of artesunate on female fertility and preimplantation embryo development, when the pregnancy is not detectable yet, artesunate was added to the oocyte in vitro maturation and in vitro embryo development of bovine. Briefly, in experiment 1 the cumulus-oocyte complexes (COCs) were in vitro matured for 18 h with 0.5, 1, or 2 µg/mL of artesunate or not (negative control) and then checked for nuclear maturation and subsequent embryo development. In experiment 2, the COCs were in vitro matured and fertilized without artesunate, which was added (0.5, 1, or 2 µg/mL) from the 1st to the 7th day of embryo culture along with a negative and a positive control group with doxorubicin. As a result, the use of artesunate on oocyte in vitro maturation did not differ from the negative control (p > 0.05) regarding nuclear maturation, cleavage, and blastocyst formation. Also, artesunate on in vitro embryo culture did not differ from negative control (p > 0.05) regarding cleavage and blastocyst formation, except for positive control, with doxorubicin (p < 0.05). In conclusion, under the conditions investigated, there was no evidence of artesunate toxicity on oocyte competence and the preimplantation period of in vitro embryo development in the bovine model, however, artesunate use still should be taken carefully as the outcome of implantation after oocytes and blastocysts exposure to artesunate remains unknown.


Artesunate added to in vitro maturation did not impair oocyte competence in bovine.Artesunate added to in vitro culture did not affect cleavage and blastocyst formation.No evidence of artesunate toxicity in oocytes and embryos of bovine was found.

20.
Int J Biometeorol ; 67(7): 1169-1183, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37171652

RESUMEN

Monitoring the climatic conditions of crops is essential for smart agriculture development and adaptation of agricultural systems in the era of global change. Thereby, it is possibly better to understand the stages of development of the crop, thus adopting management practices more efficiently and planning the harvest with greater accuracy. This study was developed to analyze the growing degree-hours and degree-days in two management zones (MZs) for each phenological stage of wheat (Triticum aestivum L.) and the application of low-cost agroclimatological stations to monitor the climatic conditions of the field production. The study was developed in a Ferralsol in Céu-Azul/Brazil. Ten low-cost agrometeorological stations were installed in two MZs delineated based on elevation data using the web platform AgDataBox. Data on solar radiation, atmospheric pressure, wind speed, precipitation, relative humidity, air, and soil temperature were evaluated over two wheat crop seasons. Our results showed different climatic conditions, especially humidity and temperature, between MZs and crop seasons, which could probably cause yield variability. By the low-cost agroclimatological stations, it is possible to collect data on the thermal accumulation by the culture in growing degree-hours, which is a more accurate parameter than the growing degree-days (commonly used in similar studies). With the growing degree-hours data, it was possible to follow the development of the phenological stages of wheat. In conclusion, the results obtained suggest the importance of evaluating agroclimatological parameters in monitoring wheat crops. However, more studies are needed in regions with greater slopes, which may have microclimates that intensely influence the crop.


Asunto(s)
Productos Agrícolas , Triticum , Estaciones del Año , Agricultura/métodos , Suelo , Cambio Climático
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