Comparative cytogenetics in four species of Palinuridae: B chromosomes, ribosomal genes and telomeric sequences

The evolutionary pathway of Palinuridae (Crustacea, Decapoda) is still controversial, uncertain and unexplored, expecially from a karyological point of view. Here we describe the South African spiny lobster Jasus lalandii karyotype: n and 2n values, heterochromatin distribution, nucleolar organizer region (NOR) location and telomeric repeat structure and location. To compare the genomic and chromosomal organization in Palinuridae we located NORs in Panulirus regius, Palinurus gilchristi and Palinurus mauritanicus: all species showed multiple NORs. In J. lalandii NORs were located on three chromosome pairs, with interindividual polymorphism. In P. regius and in the two Palinurus species NORs were located on two chromosome pairs. In the two last species 45S ribosomal gene loci were also found on B chromosomes. In addition, the nature and location of telomeric repeats were investigated by FISH in J. lalandii, P. gilchristi, P. mauritanicus Palinurus elephas, and P. regius (Palinuridae, Achelata), and in Scyllarus arctus (Scyllaridae, Achelata): all these Achelata species showed the (TTAGG)n pentameric repeats. Furthermore, in J. lalandii these repeats occurred in all the telomeres and in some interstitial chromosomal sites, associated with NORs

HIV-1 drug resistance in recently HIV-infected pregnant mother's naïve to antiretroviral therapy in Dodoma urban, Tanzania

HIV resistance affects virological response to therapy and efficacy of prophylaxis in mother-to-child-transmission. The study aims to assess the prevalence of HIV primary resistance in pregnant women naïve to antiretrovirals

A population genomics insight by 2b‐RAD reveals populations' uniqueness along the Italian coastline in Leptopsammia pruvoti (Scleractinia, Dendrophylliidae)

Aim Marine bioconstructions such as coralligenous formations are hotspot of biodiversity and play a relevant ecological role in the preservation of biodiversity by providing carbon regulation, protection and nursery areas for several marine species. For this reason, the European Union Habitat Directive included them among priority habitats to be preserved. Although their ecological role is well established, connectivity patterns are still poorly investigated, representing a limit in conservation planning. The present study pioneers a novel approach for the analysis of connectivity in marine bioconstructor species, which often lack suitable genetic markers, by taking advantage of next‐generation sequencing techniques. We assess the geographical patterns of genomic variation of the sunset cup coral Leptopsammia pruvoti Lacaze‐Duthiers, 1897, an ahermatypic, non‐zooxanthellate and solitary scleractinian coral species common in coralligenous habitats and distributed across the Mediterranean Sea. Location The Italian coastline (Western and Central Mediterranean). Methods We applied the restriction site‐associated 2b‐RAD approach to genotype over 1,000 high‐quality and filtered single nucleotide polymorphisms in 10 population samples. Results The results revealed the existence of a strongly supported genetic structure, with highly significant pairwise FST values between all the population samples, including those collected about 5 km apart from each other. Moreover, genomic data indicate that the strongest barriers to gene flow are between the western (Ligurian–Tyrrhenian Sea) and the eastern side (Adriatic Sea) of the Italian peninsula. Main conclusions The strong differentiation found in L. pruvoti is similar to that found in other species of marine bioconstructors investigated in this area, but it strongly contrasts with the small differences found in many fish and invertebrates at the same geographical scale. All in one, our results highlight the importance of assessing connectivity in species belonging to coralligenous habitats as, due to their limited dispersal ability, they might require specific spatial conservation measures

A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G

Introduction: A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection. Materials and Methods: We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy). Results: HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 – 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3’UTR polymorphism (rs371194629) shows that the HLA-G 3’UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X2 = 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X2 = 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3’UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 – 0.7), PM = 6.5 x 10-4]. Conclusion: Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients

The double-sided of human leukocyte antigen-G molecules in type 1 autoimmune hepatitis

The immunomodulatory effects of HLA-G expression and its role in cancers, human liver infections and liver transplantation are well documented, but so far, there are only a few reports addressing autoimmune liver diseases, particularly autoimmune hepatitis (AIH). Method and materialsWe analyzed the genetic and phenotypic characteristics of HLA-G in 205 type 1 AIH patients (AIH-1) and a population of 210 healthy controls from Sardinia (Italy). ResultsAnalysis of the HLA-G locus showed no substantial differences in allele frequencies between patients and the healthy control population. The HLA-G UTR-1 haplotype was the most prevalent in both AIH-1 patients and controls (40.24% and 34.29%). Strong linkage was found between the HLA-G UTR-1 haplotype and HLA-DRB1*03:01 in AIH-1 patients but not controls (D' = 0.92 vs D' = 0.50 respectively; P = 1.3x10(-8)). Soluble HLA-G (sHLA-G) levels were significantly lower in AIH-1 patients compared to controls [13.9 (11.6 - 17.4) U/mL vs 21.3 (16.5 - 27.8) U/mL; P = 0.011]. Twenty-four patients with mild or moderate inflammatory involvement, as assessed from liver biopsy, showed much higher sHLA-G levels compared to the 28 patients with severe liver inflammation [33.5 (23.6 - 44.8) U/mL vs 8.8 (6.1 - 14.5) U/mL; P = 0.003]. Finally, immunohistochemistry analysis of 52 liver biopsies from AIH-1 patients did not show expression of HLA-G molecules in the liver parenchyma. However, a percentage of 69.2% (36/52) revealed widespread expression of HLA-G both in the cytoplasm and the membrane of plasma cells labeled with anti-HLA-G monoclonal antibodies. ConclusionThis study highlights the positive immunomodulatory effect of HLA-G molecules on the clinical course of AIH-1 and how this improvement closely correlates with plasma levels of sHLA-G. However, our results open the debate on the ambiguous role of HLA-G molecules expressed by plasma cells, which are pathognomonic features of AIH-1

Natural killer-cell immunoglobulin-like receptors trigger differences in immune response to SARS-CoV-2 infection

Background: The diversity in the clinical course of COVID-19 has been related to differences in innate and adaptative immune response mechanisms. Natural killer (NK) lymphocytes are critical protagonists of human host defense against viral infections. It would seem that reduced circulating levels of these cells have an impact on COVID-19 progression and severity. Their activity is strongly regulated by killer-cell immuno-globulin-like receptors (KIRs) expressed on the NK cell surface. The present study's focus was to investigate the impact of KIRs and their HLA Class I ligands on SARS-CoV-2 infection. Methods: KIR gene frequencies, KIR haplotypes, KIR ligands and combinations of KIRs and their HLA Class I ligands were investigated in 396 Sardinian patients with SARS-CoV-2 infection. Comparisons were made between 2 groups of patients divided according to disease severity: 240 patients were symptomatic or paucisymptomatic (Group A), 156 hospitalized patients had severe disease (Group S). The immunogenetic characteristics of patients were also compared to a population group of 400 individuals from the same geographical areas. Results: Substantial differences were obtained for KIR genes, KIR haplotypes and KIR-HLA ligand combinations when comparing patients of Group S to those of Group A. Patients in Group S had a statistically significant higher frequency of the KIR A/A haplotype compared to patients in Group A [34.6% vs 23.8%, OR = 1.7 (95% CI 1.1-2.6); P = 0.02, Pc = 0.04]. Moreover, the KIR2DS2/HLA C1 combination was poorly represented in the group of patients with severe symptoms compared to those of the asymptomatic-paucisymptomatic group [33.3% vs 50.0%, OR = 0.5 (95% CI 0.3-0.8), P = 0.001, Pc = 0.002]. Multivariate analysis confirmed that, regardless of the sex and age of the patients, the latter genetic variable correlated with a less severe disease course [ORM = 0.4 (95% CI 0.3-0.7), PM = 0.0005, PMC = 0.005]. Conclusions: The KIR2DS2/HLA C1 functional unit resulted to have a strong protective effect against the adverse outcomes of COVID-19. Combined to other well known factors such as advanced age, male sex and concomitant autoimmune diseases, this marker could prove to be highly informative of the disease course and thus enable the timely intervention needed to reduce the mortality associated with the severe forms of SARS-CoV-2 infection. However, larger studies in other populations as well as experimental functional studies will be needed to confirm our findings and further pursue the effect of KIR receptors on NK cell immune-mediated response to SARS-Cov-2 infection

Integrating green infrastructure and ecological corridors: A study concerning the Metropolitan Area of Cagliari (Italy)

Green Infrastructure (GI) is defined as a network of natural and semi-natural areas that need to be planned in a strategic way to deliver ecosystem services (ESs). This definition highlights two important concepts: multifunctionality and connectivity. Multifunctionality concerns the capacity of a single area to deliver several benefits and to perform multiple functions. The concept of connectivity is often linked to ecological corridors (ECs), defined as spatial elements that connect habitats, allowing species migration and genetic exchange. Consequently, the spatial identification of GIs and ECs in spatial planning is a noteworthy topic. In this study, we propose a methodological approach to identify a multifunctional GI and ECs connecting Natura 2000 sites (N2Ss) in the case study of the Metropolitan City of Cagliari, Italy, in relation to three steps. The first, based on a previous work of Arcidiacono et al. (2016), concerns the spatial configuration of a multifunctional GI in relation to four aspects (conservation value, natural value, recreational value and anthropic heritage). The second step concerns the identification of potential ECs in relation to two concepts, habitat suitability and ecological integrity, integrated through a resistance map. The last step aims at assessing the likelihood of inclusion of the ECs, identified in the second step, within a metropolitan GI in relation to the taxonomy developed in the first step. In other words, we intend to assess if and to what extent the Natura 2000 network can be considered a part of a metropolitan GI

Forecasting cycle time in semiconductor manufacturing systems: a literature review

An efficient and effective forecasting of production cycle times (CT) is a critical success factor in semiconductor manufacturing systems (SMS): inaccurate CT forecasts can have a negative impact on production scheduling, causing late deliveries, as well as on the amount of inventories and work-in-progress, which rapidly lose value over time because of the high risk of obsolescence. Therefore, since the 80s, several quantitative techniques have been developed to face this problem. Furthermore, Artificial Intelligence (AI) techniques are gaining importance, despite their potential is still not fully exploited even in the most advanced manufacturing systems. However, a synthetic overview of the techniques to forecast CT in SMS is still missing in the literature. As a result, it is difficult for decision makers to orient themselves and choose, among the many existing ones, the best model for their specific situation, comparing the different performance in terms of accuracy, data required, speed and easiness to use. This paper aims at presenting an overview of the quantitative techniques developed to forecast production CT in SMS. Firstly, a description of the methodology with which the literature review has been carried out is provided. Secondly, a taxonomy of forecasting techniques is proposed. Subsequently, a synthetic description of analytical, simulation, time-series and causal methods is presented. Within statistical techniques, a special focus is deserved to AI ones, since their popularity has dramatically increased in the last years. In particular, the most recent applications of artificial neural networks (ANN) in SMS – namely, hybrid methods and Long-Short-Term-Memory recursive neural networks – are described. Finally, a table with a qualitative comparison between the different methods is proposed.11-13 September 201

Localization of the pentanucleotide telomeric sequence (TTAGG)n in crustacean decapods

Localization of the pentanucleotide telomeric sequence (TTAGG)n in crustacean decapods. Coluccia E., Salvadori S., Deidda F., Cannas R., Deiana A.M. Dipartimento di Biologia Animale ed Ecologia, Università di Cagliari, V.le Poetto, 1- 09126 Cagliari, Italy. Telomeres are highly specialized DNA-protein structures that cap eukaryotic chromosome ends. They have a number of functions allowing complete replication at the end of a linear DNA molecule, preventing chromosomal degradation and end-to-end fusion. Although the sequence of the telomeric repeat differs among different organisms, some sequences are conserved in whole taxonomic groups; in fact the human telomere consensus sequence (TTAGGG)n is highly conserved among vertebrates, and the (TTTAGGG)n sequence is frequently found in plants. Telomeres of most invertebrate species have yet to be isolated, although among arthropods different types of telomere sequences have been reported, and the pentanucleotide (TTAGG) motif seems to be widespread among insects and present in other artropods, including crustaceans. In this study, fluorescence in situ hybridization (FISH) technique was used to determine the telomeric sequence in some species of lobsters belonging to the Palinuridae and Nephropidae families (Crustacea, Decapoda). Mitotic and meiotic chromosomes were prepared from gonads of adult males by the air-drying technique. Both the human TTAGGG repeat and the TTAGG repeat were used as probe. No hybridization signals were detected with the TTAGGG hexanucleotide repeated sequence; whereas strong signals were observed at the end of the chromosomes with the TTAGG pentanucleotide repeated sequence. These findings are in accordance with the hypotesis that the pentanucletide TTAGG is an ancestral motif of telomeres for arthropods. In fact the TTAGG repeat is widely conserved among insect species and hybridized to DNAs from other arthropods