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Article: The good, the bad and the ugly of transposable elements annotation tools.

Loreto, Elgion L S / Melo, Elverson S de / Wallau, Gabriel L / Gomes, Tiago M F F

2024 Volume 46, Issue 3 Suppl 1, Page(s) e20230138

Abstract: Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many ... ...

Abstract	Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions.
Language	English
Publishing date	2024-02-19
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	1445712-x
ISSN	1678-4685 ; 1415-4757
ISSN (online)	1678-4685
ISSN	1415-4757
DOI	10.1590/1678-4685-GMB-2023-0138
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Article: Exploring Natural Variations in

Lombardi, Marco / Bellucci, Manuel / Cimini, Sara / Locato, Vittoria / Loreto, Francesco / De Gara, Laura

Plants (Basel, Switzerland)

2024 Volume 13, Issue 8

Abstract: The increase in soil salinization represents a current challenge for plant productivity, as most plants, including crops, are mainly salt-sensitive species. The identification of molecular traits underpinning salt tolerance represents a primary goal for ... ...

Abstract	The increase in soil salinization represents a current challenge for plant productivity, as most plants, including crops, are mainly salt-sensitive species. The identification of molecular traits underpinning salt tolerance represents a primary goal for breeding programs. In this scenario, the study of intraspecific variability represents a valid tool for investigating natural genetic resources evolved by plants in different environmental conditions. As a model system,
Language	English
Publishing date	2024-04-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants13081069
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Article ; Online: Multiple long-range host shifts of major Wolbachia supergroups infecting arthropods.

Gomes, Tiago M F F / Wallau, Gabriel L / Loreto, Elgion L S

Scientific reports

2022 Volume 12, Issue 1, Page(s) 8131

Abstract: Wolbachia is a genus of intracellular bacterial endosymbionts found in 20-66% of all insect species and a range of other invertebrates. It is classified as a single species, Wolbachia pipientis, divided into supergroups A to U, with supergroups A and B ... ...

Abstract	Wolbachia is a genus of intracellular bacterial endosymbionts found in 20-66% of all insect species and a range of other invertebrates. It is classified as a single species, Wolbachia pipientis, divided into supergroups A to U, with supergroups A and B infecting arthropods exclusively. Wolbachia is transmitted mainly via vertical transmission through female oocytes, but can also be transmitted across different taxa by host shift (HS): the direct transmission of Wolbachia cells between organisms without involving vertically transmitted gametic cells. To assess the HS contribution, we recovered 50 orthologous genes from over 1000 Wolbachia genomes, reconstructed their phylogeny and calculated gene similarity. Of 15 supergroup A Wolbachia lineages, 10 have similarities ranging from 95 to 99.9%, while their hosts' similarities are around 60 to 80%. For supergroup B, four out of eight lineages, which infect diverse and distantly-related organisms such as Acari, Hemiptera and Diptera, showed similarities from 93 to 97%. These results show that Wolbachia genomes have a much higher similarity when compared to their hosts' genes, which is a major indicator of HS. Our comparative genomic analysis suggests that, at least for supergroups A and B, HS is more frequent than expected, occurring even between distantly-related species.
MeSH term(s)	Animals ; Arthropods/genetics ; Arthropods/microbiology ; Female ; Insecta/microbiology ; Phylogeny ; Wolbachia/genetics
Language	English
Publishing date	2022-05-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-12299-x
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Article ; Online: The evolution of diffusive and biochemical capacities for photosynthesis was predominantly shaped by [CO

Haworth, Matthew / Marino, Giovanni / Loreto, Francesco / Centritto, Mauro

The Science of the total environment

2022 Volume 840, Page(s) 156606

Abstract: The atmospheric concentration of carbon dioxide ([ ... ...

Abstract	The atmospheric concentration of carbon dioxide ([CO
MeSH term(s)	Atmosphere ; Carbon Dioxide ; Oxygen ; Photosynthesis ; Plant Leaves/metabolism ; Plants/metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism
Chemical Substances	Carbon Dioxide (142M471B3J) ; Ribulose-Bisphosphate Carboxylase (EC 4.1.1.39) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-06-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.156606
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Article ; Online: Gender representation in science publication: evidence from

Marescotti, Manuela / Loreto, Flavia / Spires-Jones, Tara L

Brain communications

2022 Volume 4, Issue 3, Page(s) fcac077

Abstract: The persistent underrepresentation of women in Science, Technology, Engineering, Mathematics and Medicine (STEMM) points to the need to continue promoting the awareness and understanding of this phenomenon. Being one of the main outputs of scientific ... ...

Abstract	The persistent underrepresentation of women in Science, Technology, Engineering, Mathematics and Medicine (STEMM) points to the need to continue promoting the awareness and understanding of this phenomenon. Being one of the main outputs of scientific work, academic publications provide the opportunity to quantify the gender gap in science as well as to identify possible sources of bias and areas of improvement.
Language	English
Publishing date	2022-03-25
Publishing country	England
Document type	Journal Article
ISSN	2632-1297
ISSN (online)	2632-1297
DOI	10.1093/braincomms/fcac077
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Article: Effectiveness, Simplification and Persistence of IDegLira in Poorly Controlled People with Type 2 Diabetes: A 4-Year Follow-Up Real-World Study.

Di Loreto, Chiara / Celleno, Roberta / Pezzuto, Debora / Ambrosi, Franca / Bellavita, Silvia / Biagini, Marinella / Passeri, Monica / Del Sindaco, Paola

Diabetes therapy : research, treatment and education of diabetes and related disorders

2024

Abstract: Introduction: Efficacy and safety of the fixed ratio combination of insulin degludec and liraglutide (IDegLira) has been largely documented. However, long-term data are limited. This study aimed at describing persistence in therapy and the effectiveness ...

Abstract	Introduction: Efficacy and safety of the fixed ratio combination of insulin degludec and liraglutide (IDegLira) has been largely documented. However, long-term data are limited. This study aimed at describing persistence in therapy and the effectiveness at 48 months of IDegLira. Methods: We conducted an observational study based on retrospective chart review. All patients treated with IDegLira during 2018-2022 were included. Data on treatment approaches and clinical outcomes were collected at the first prescription of IDegLira (T0) and after 6, 12, 24, 36, and 48 months. Results: Overall, 156 patients (mean age 68 years, 64.1% men) started IDegLira, of whom 88 (56.4%) were previously treated with basal-oral therapy (BOT) and 68 (43.6%) with basal-bolus schemes (BB). Before starting IDegLira, 23.8% were treated with ≥ 2 oral antihyperglycemic agents in association with insulin; at T0, the proportion decreased to 3.2%. Short-acting insulin was discontinued after the first week. After 48 months, levels of HbA1c were significantly reduced by 1.34% in the BOT group and 1.07% in the BB group (p < 0.0001 in both groups). In the BOT group, FBG levels decreased by about 50 mg/dl and body weight was unchanged. In the BB group, FBG levels decreased by about 40 mg/dl and body weight was significantly reduced by an average of 7.7 kg. Five patients (3.2%) interrupted therapy with IDegLira during 48 months, and no severe hypoglycemia occurred. Conclusions: Our study emphasizes the important role of IDegLira in maintaining a good metabolic control while minimizing the risk of major hypoglycemia and weight gain in the long term. The substantial simplification of treatment schemes can increase adherence.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2566702-6
ISSN	1869-6961 ; 1869-6953
ISSN (online)	1869-6961
ISSN	1869-6953
DOI	10.1007/s13300-024-01564-z
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Article ; Online: Integrating stomatal physiology and morphology: evolution of stomatal control and development of future crops.

Haworth, Matthew / Marino, Giovanni / Loreto, Francesco / Centritto, Mauro

Oecologia

2021 Volume 197, Issue 4, Page(s) 867–883

Abstract: Stomata are central players in the hydrological and carbon cycles, regulating the uptake of carbon dioxide ( ... ...

Abstract	Stomata are central players in the hydrological and carbon cycles, regulating the uptake of carbon dioxide (CO
MeSH term(s)	Atmosphere ; Carbon Dioxide ; Photosynthesis ; Plant Leaves ; Plant Stomata
Chemical Substances	Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2021-01-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	123369-5
ISSN	1432-1939 ; 0029-8549
ISSN (online)	1432-1939
ISSN	0029-8549
DOI	10.1007/s00442-021-04857-3
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Article ; Online: Isoprene Emission Influences the Proteomic Profile of Arabidopsis Plants under Well-Watered and Drought-Stress Conditions.

Mancini, Ilaria / Domingo, Guido / Bracale, Marcella / Loreto, Francesco / Pollastri, Susanna

International journal of molecular sciences

2022 Volume 23, Issue 7

Abstract: Isoprene is a small lipophilic molecule synthesized in plastids and abundantly released into the atmosphere. Isoprene-emitting plants are better protected against abiotic stresses, but the mechanism of action of isoprene is still under debate. In this ... ...

Abstract	Isoprene is a small lipophilic molecule synthesized in plastids and abundantly released into the atmosphere. Isoprene-emitting plants are better protected against abiotic stresses, but the mechanism of action of isoprene is still under debate. In this study, we compared the physiological responses and proteomic profiles of Arabidopsis which express the isoprene synthase (ISPS) gene and emit isoprene with those of non-emitting plants under both drought-stress (DS) and well-watered (WW) conditions. We aimed to investigate whether isoprene-emitting plants displayed a different proteomic profile that is consistent with the metabolic changes already reported. Only ISPS DS plants were able to maintain the same photosynthesis and fresh weight of WW plants. LC-MS/MS-based proteomic analysis revealed changes in protein abundance that were dependent on the capacity for emitting isoprene in addition to those caused by the DS. The majority of the proteins changed in response to the interaction between DS and isoprene emission. These include proteins that are associated with the activation of secondary metabolisms leading to ABA, trehalose, and proline accumulations. Overall, our proteomic data suggest that isoprene exerts its protective mechanism at different levels: under drought stress, isoprene affects the abundance of chloroplast proteins, confirming a strong direct or indirect antioxidant action and also modulates signaling and hormone pathways, especially those controlling ABA synthesis. Unexpectedly, isoprene also alters membrane trafficking.
MeSH term(s)	Arabidopsis/genetics ; Arabidopsis/metabolism ; Butadienes/metabolism ; Butadienes/pharmacology ; Chromatography, Liquid ; Droughts ; Hemiterpenes/metabolism ; Pentanes/metabolism ; Photosynthesis ; Proteomics ; Stress, Physiological ; Tandem Mass Spectrometry ; Water/metabolism
Chemical Substances	Butadienes ; Hemiterpenes ; Pentanes ; Water (059QF0KO0R) ; isoprene (0A62964IBU)
Language	English
Publishing date	2022-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23073836
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Article ; Online: Determinants of root system architecture for future-ready, stress-resilient crops.

Lombardi, Marco / De Gara, Laura / Loreto, Francesco

Physiologia plantarum

2021 Volume 172, Issue 4, Page(s) 2090–2097

Abstract: Climate change hampers food safety and food security. Crop breeding has been boosting superior quantity traits such as yield, but roots have often been overlooked in spite of their role in the whole plant physiology. New evidence is emerging on the ... ...

Abstract	Climate change hampers food safety and food security. Crop breeding has been boosting superior quantity traits such as yield, but roots have often been overlooked in spite of their role in the whole plant physiology. New evidence is emerging on the relevance of root system architecture in coping with the environment. Here, we review determinants of root system architecture, mainly based on studies on Arabidopsis, and we discuss how breeding for appropriate root architecture may help obtain plants that are better adapted or resilient to abiotic and biotic stresses, more productive, and more efficient for soil and water use. We also highlight recent advances in phenotyping high-tech platforms and genotyping techniques that may further help to understand the mechanisms of root development and how roots control relationships between plants and soil. An integrated approach is proposed that combines phenotyping and genotyping information via bioinformatic analyses and reveals genetic control of root system architecture, paving the way for future research on plant breeding.
MeSH term(s)	Crops, Agricultural/genetics ; Plant Breeding ; Plant Roots/genetics ; Soil ; Stress, Physiological
Chemical Substances	Soil
Language	English
Publishing date	2021-05-07
Publishing country	Denmark
Document type	Journal Article ; Review
ZDB-ID	2020837-6
ISSN	1399-3054 ; 0031-9317
ISSN (online)	1399-3054
ISSN	0031-9317
DOI	10.1111/ppl.13439
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Article: Should we enlarge the indication for kidney biopsy in patients with diabetes? The pro part.

Gesualdo, Loreto / Fiorentino, Marco / Conserva, Francesca / Pontrelli, Paola

Clinical kidney journal

2023 Volume 17, Issue 1, Page(s) sfad266

Abstract: Diabetic nephropathy (DN) and non-diabetic renal diseases (NDRD) represent intricate challenges in diagnosis and treatment within the context of the global diabetes epidemic. As the prevalence of diabetes continues to escalate, effective management of ... ...

Abstract	Diabetic nephropathy (DN) and non-diabetic renal diseases (NDRD) represent intricate challenges in diagnosis and treatment within the context of the global diabetes epidemic. As the prevalence of diabetes continues to escalate, effective management of renal complications becomes paramount. Recent advancements in comprehending the multifaceted nature of renal damage, fueled by insights from histopathological investigations, offer unprecedented prospects for refining diagnostic strategies and customizing therapeutic interventions. Renal biopsies have emerged as indispensable tools for unraveling the diverse phenotypes of renal damage in diabetes. The pioneering study by Mazzucco identified three classes of renal damage in type 2 diabetes patients: classical diabetic glomerulosclerosis (DN), vascular and ischemic glomerular changes (NDRD), and other glomerulonephritides in the presence (DN + NDRD, mixed forms) or absence of DN (NDRD). The prevalence of these classes varies widely in published studies, influenced by factors such as ethnicity, geography and selection criteria for renal biopsy. Moreover, the international Renal Pathology Society consensus classification system has stratified the classical diabetic nephropathy into progressive categories of renal impairment, a breakthrough that aids in prognostication. Histopathological scrutiny, particularly the intricate correlation between glomerular and tubulointerstitial lesions, contributes profoundly to enhancing our grasp of the phenotype's heterogeneity. This amplified comprehension holds the potential to steer personalized treatment strategies. Cutting-edge interventions, encompassing sodium-glucose cotransporter 2 inhibitors, mineralocorticoid receptor antagonists and anti-endothelin receptor agents, are broadening the arsenal against renal injury in diabetes. When combined with the profound insights garnered from histopathological, omics, imaging and clinical data, these therapeutic avenues promise a transformative shift towards precision-driven care paradigms. Collaborative efforts uniting researchers, clinicians and patients are indispensable for propelling our knowledge of diabetic renal damage and ameliorating patient outcomes. The fusion of histopathological, omics and imaging findings into clinical decision-making harbors the potential to customize interventions and optimize care for individuals grappling with diabetes-associated renal complications. Furthermore, groundbreaking initiatives like the iBeat Study within the BEAt-DKD (Biomarker Enterprise to Attack Diabetic Kidney Disease) project (https://www.beat-dkd.eu/), elucidating distinct phenotypes of renal damage within diabetes, underscore the imperative necessity of integrating histopathological data into the broader framework of diabetic renal management.
Language	English
Publishing date	2023-10-26
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2655800-2
ISSN	2048-8513 ; 2048-8505
ISSN (online)	2048-8513
ISSN	2048-8505
DOI	10.1093/ckj/sfad266
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