FISH Technique Research Articles

Using Social Media Platforms to Study the Ecology and Exploitation of Mud Lobsters in the Philippines

Mud lobsters are burrowing crustaceans that are widely distributed in the Indo-Pacific region, including the Philippines. However, they are somehow neglected in scientific studies in the country. The increasing risks brought by this pandemic further impede field surveys as mobilization is highly regulated. Hence, the use of social media platforms was explored to study the ecology and exploitation of mud lobsters in the Philippines. This study used content analysis of YouTube videos. Key terms were searched to identify contents such as 'Philippines,' 'mud lobsters,' and local terms like 'bulaso,' 'uson,' and 'urong.' A total of 30 videos were analyzed. Videos were posted from 2015–2021 from at least 10 provinces. Results reinforce the already known wide distribution of mud lobsters in mangrove forests, fishponds, and rice fields beside mangroves. Still, there were notable mud lobster behaviors observed such as 1) surfacing during the rainy season, 2) the timing of which disturbed burrow is repaired, and 3) conspecific repulsion – all of which were not previously documented. Empty burrows were also found inhabited by the terrestrial crab Cardisoma carnifex. Mud lobsters were commonly caught using bamboo traps, but some had developed unique fishing techniques such as mound disturbance and the tali-tali method. Alarmingly, this study also found the use of toxic chemicals for illegal fishing activity. This study provides evidence on the potential use of social media to study aquatic organisms. Additional knowledge on mud lobster ecology and baseline information on some aspects of its fishery in the Philippines was observed. Social media can be useful for surveillance and ecological studies but could not be used as an alternative method for in-depth biological and taxonomic studies, where actual specimens are necessary.

Diagnostic Utility of Multimodal Genomic Profiling for Molecular Classification and MRD Assessment in Adult B-Cell Acute Lymphoblastic Leukemia

Genomic markers define molecular subtypes and measurable residual disease (MRD) targets in B-cell acute lymphoblastic leukemia/lymphoma (B-ALL) and are essential determinants of treatment. Current diagnostic approaches typically involve serial multi-step testing utilizing conventional cytogenetics (CC)/FISH and molecular genetic (RT-qPCR, MLPA, clonality PCR, NGS panel) techniques which are time and sample consuming and ultimately may not adequately identify genomically complex B-ALL subtypes. In contrast, single-step comprehensive genomic profiling by whole genome and whole transcriptome sequencing (WGS/WTS) may be more efficient for the molecular classification of established and newly described entities which are of increasing therapeutic relevance. We have instituted a multimodal platform for molecular testing in B-ALL performing WGS/WTS in parallel with deep NGS-based immunoglobulin (IG) rearrangement MRD and exploratory DNA-breakpoint based MRD assays. We aimed to determine the utility of this approach for subtype classification compared to a standard-of-care diagnostic approach of CC/FISH testing.Forty-two consecutive adult patients underwent both standard-of-care diagnostic testing and WGS/WTS. 20/42 (48%) patients had an abnormal CC/FISH result supporting classification into recognized molecular subgroups. WGS/WTS assessment incorporating somatic coding and non-coding mutations, structural variants, fusions, copy number abnormalities and gene expression subtype prediction (ALLSorts, https://github.com/Oshlack/ALLSorts) was performed with concordant results in all 20 patients. 16/22 patients that were unclassified by CC/FISH were successfully reclassified by WGS/WTS including subtypes enriched for cryptic rearrangements (Ph-like, DUX4, MEF2D) and groups characterized by heterogeneous genomic alterations or a distinctive gene expression signature (PAX5alt, ZEB2/CEBP). A low hypodiploid karyotype was observed in two cases with an apparently normal karyotype by CC. The six patients who remained without a subtype defining driver genetic alteration after comprehensive testing frequently harbored novel IGH translocations or a Ph-like expression signature but without a described fusion.In order to understand the relative contribution from WGS versus WTS, analysis of 36 patients was performed using a truth classification. WGS and WTS produced equivalent classifications for 22 cases. Two cases were based solely on WGS findings (iAMP21 and ZEB2/CEBP) and three cases were based solely on WTS findings (DUX4). Importantly the combination of both WGS and WTS was critical to correctly classify nine cases (Ph-like and PAX5alt).MRD was assessed by a sensitive NGS assay to IG rearrangements (Adaptive Biotechnologies) and by quantitative probe-based droplet digital PCR (ddPCR) assays designed to structural rearrangement DNA breakpoints from genome data (analytical sensitivity 10 -4). Patient-specific ddPCR assays were designed to eight structural variants (KMT2A and IGH translocations, and IKZF1 deletions) in seven patients and assessed in 36 remission samples with parallel testing by multiparametric flow cytometry (MFC). Concordant MFC and ddPCR was observed in 30/36 samples (19 MRD pos, 11 MRD neg). Discordances included two MRD pos by MFC-only and four MRD pos by ddPCR-only; the latter often occurring in the setting of antigen directed therapy or in ALL with a less informative immunophenotype, demonstrating the additional utility of non-MFC based MRD assessment in specific clinical settings. 27/42 patients in our cohort had ≥1 genomic structural rearrangement identified by WGS that could be used for patient-specific MRD monitoring to complement existing MRD assessment.In conclusion WGS/WTS provided a molecular subtype classification in 86% of our cohort compared to 48% by standard-of-care diagnostic testing highlighting that CC/FISH alone is inadequate for contemporary molecular classification of B-ALL, which may have implications for treatment decisions. Importantly, the combination of WGS and WTS was superior to WGS-only or WTS-only for correct molecular subtype assignment. This approach has the potential to improve risk assessment in adult B-ALL and the routine feasibility, improvement in clinical outcomes and health economic impact warrant further assessment. DisclosuresBajel: Abbvie, Amgen, Novartis, Pfizer: Honoraria; Amgen: Speakers Bureau. Dickinson: Janssen: Consultancy, Honoraria; Amgen: Honoraria; Celgene: Research Funding; Gilead Sciences: Consultancy, Honoraria, Speakers Bureau; MSD: Consultancy, Honoraria, Research Funding, Speakers Bureau; Takeda: Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria; Roche: Consultancy, Honoraria, Other: travel, accommodation, expenses, Research Funding, Speakers Bureau; Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau. Tiong: Servier: Consultancy, Speakers Bureau; Amgen: Speakers Bureau; Pfizer: Consultancy.

Fishing techniques and gears developed by tribal communities around Bargi Reservoir in Madhya Pradesh, India

Traditional knowledge (TK) plays very important role in the millions of people around the world. There is immense need of documentation of traditional knowledge especially in countries rich in biodiversity, such as India. Bargi is one of the major dam constructed on river Narmada in Madhya Pradesh. Local communities use various fishing methods since time memorable. Dam changes ecology and hydrology of river. Tribal communities have adapted their fishing techniques to these changes and have also developed new techniques. Fishing technique described is this paper practiced around Bargi Reservoir. Six type of crafts and different gears were encountered during the two years of seasonal survey.

Production and Disruptions of Prawn and Crab: Basis for Supply Chain Management Strategies

Supply chain management strategies will help the prawn and crab growers mitigate and adapt to the impact of various disruptions such as typhoons, water-borne diseases, and climate change. The study was conducted to determine the production and disruptions and prawn and crab basis for supply chain management strategies of the growers. The study employed a descriptive research design using quantitative data. The study used secondary data for performance and disaster history. A content analysis was used in processing the data. The researchers validated the findings and results of the study, and a random interview was conducted. Findings revealed that disruptions affect the production of prawn and crab, growers have their fishing technique and management practices, supply chain management strategies were not prioritized for value-adding and technology accessibility. A supply chain management strategy may be employed to operate and produce prawns and crabs in the Province of Capiz to achieve profitability and sustainability. It should be noted that the data is from 2011 to 2017. The data coverage is the Province of Capiz and focuses on the volume and value of prawns and crab (tiger prawn, endeavor prawn, and mud crab).

Traditional fishing methods used by the fishermen in the Sundarban region, West Bengal

In 2020-2021, 14 Blocks out of 19 Blocks in the Indian Sundarban regions studied fishing methods. According to our study, current socio-economic circumstances in Indian Sundarban regions show that their lifestyle is unsuitable for low family income. This is due to large annual disasters such as cyclones, storms, floods, and the water's salinity. A network of rivers and canals connects the Sundarban. The majority of the population is reliant on fishing activity, and in particular, the livelihood of the local people is supported by capture fisheries, which are in turn reliant on fishing activity. During the study, fishers' homes received knowledge about various crafts and equipment through monthly visits. Fishers have used indigenous fishing techniques and gear in the Indian Sundarban areas to capture fish, increasingly contributing to the local economy and overall fish output. During the research period, five different kinds of crafts and twelve different kinds of gear were found. The study reveals different indigenous fishing gears used in the locality, such as nets, traps, lines and hooks. To catch various fish of various sizes, fishers employ a variety of fishing gears, each with a distinct form and size. Most fishermen in the area collect unripe fruits velvet apple (Diospyros sp.) from the forest and boil them in large pots with sufficient water. Nets and other traps are dried in the sun after being polished with an extract. The purpose of this article is to document fishery-related technical knowledge, particularly traditional fishing techniques and gears utilised in the Indian Sundarban area.

Post-release survival and prolonged sublethal effects of capture and barotrauma on deep-dwelling rockfishes (genus Sebastes): implications for fish management and conservation

Abstract Barotrauma—injury induced by changes in pressure—is a widespread challenge for successfully releasing fishes following capture. We used acoustic telemetry to examine the long-term post-release survival and behaviour of four rockfish species (genus Sebastes) suffering from barotrauma following capture using recreational fishing techniques. We placed particular emphasis on examining Cowcod (Sebastes levis) and Bocaccio (Sebastes paucispinis), two historically overfished species along the United States West Coast that serve as good model species representing different ecological lifestyles. We show that fish survival was species specific and that 40% of observed mortality occurred more than 48 h post release—a typical time period used in many short-term survivorship studies. Cowcod survival was correlated with fish length, sea surface temperature, and dissolved oxygen concentration at the mean depth of capture. Generalized additive mixed models of Cowcod and Bocaccio behaviour showed that surviving individuals were negatively affected by capture and barotrauma for at least 30 d post-release. Our findings demonstrate the need for extended observations to accurately quantify the mortality of fishes suffering from barotrauma and show how such data can be successfully implemented into fisheries management through engagement between managers, scientists, and the fishing community.

Türkiye’deki barbungiller balıkçılığının TÜİK mikro-veri setine dayalı olarak değerlendirilmesi

Although goatfishes (Mullidae Rafinesque, 1815) are among the most important commercial fishes in Turkey, no research has been found investigating the characteristics and spatial patterns of goatfish fishery. Here, we assessed the goatfish fishery of Turkey based on the microdata set of Turkish National Fishery Statistics gathered by Turkish Statistical Institute (TÜİK) between 2014 and 2017. In this context, we investigated the variation of total goatfish catch by cities. In addition, we compared the contribution of small (boat <10m) and large scale (boat >10m) fishers as well as different fishing techniques to the total goatfish catch in Turkey. Finally, an evaluation was made on the discard rates recorded in the official landing statistics. The results showed that higher red mullet (Mullus barbatus Linnaeus, 1758) catch was reported in the eastern Mediterranean, whereas surmullet (Mullus surmuletus Linnaeus, 1758) catch was significantly higher in the western Black Sea. On the other hand, fishery-independent investigations revealed that the Turkish fishery fleet mostly catches red mullet throughout the coasts of Turkey. Therefore, the separate records of red mullet and surmullet in the landing statistics likely represent the local names of red mullet rather than two different species. Large scale fishers were the main source of fishery pressure in the Mediterranean Sea, the Aegean Sea and the Black Sea. However, the majority of the catch was landed by small scale fishers in the Marmara Sea. The bottom trawl fishery landed 88, 92 and 87% of total goatfish catch in the Black Sea, the Aegean Sea and the Mediterranean Sea, respectively. Purse seiners provided the largest part of total goatfish catch (40%) in the Marmara Sea, where the bottom trawl fishery is prohibited. The overall average for the discard rate was found to be 0.47%. There were no statistically significant differences among the discard rates of two species, marine regions or fishing methods.

Bio-Inspired Design, Modeling, and Control of Robotic Fish Propelled by a Double-Slider-Crank Mechanism Driven Tail

Abstract This paper presents the design, modeling, and control of a three-joint robotic fish propelled by a double-slider-crank (DSC) driven caudal fin. DSC is a mechanism that can use one direct current motor to achieve oscillating foil propulsion. Its design is guided by a traveling wave equation that mimics a fish's undulatory locomotion. After multiple tests, the robotic fish displayed good performance in mimicking a real fish's swimming motion. DSC mechanism is proven to be an effective propulsion technique for a robotic fish. With the help of another servomotor at the first joint of the fish's tail, the robotic fish can have a two-dimensional free-swimming capability. In experiments, the robotic fish can achieve a swimming speed of 0.35 m/s at 3 Hz, equivalent to 0.98 body length (BL) per second. Its steering rate is proportional to a bias angle. The DSC benefits the control of the robotic fish by independently adjusting its steering and swimming speed. This characteristic is studied in a hydrodynamic model that derives the thrust within a DSC frame. Besides the dynamic model, a semiphysics-based and data-driven linear model is established to connect bias angle to robotic fish's heading angle. The linear model is used for designing an observed-state feedback control control, and the controller has been examined in simulation and experiments.

Livelihoods of Otter fishers` in the South-Western zone of Bangladesh

Fishing with otters is an ancient fishing technique in Bangladesh, exists only in the south-western part of the country with smooth-coated Otter (Lutrogale perspicillata). The present study was carried out to portray this unique fishing technique and to investigate otter fishers` livelihood status in Narail District. Fishing with otters is carried out at night in the Chitra and the Nabaganga rivers, involving at least four people, a boat, a net, 2-3 adult tamed otters and 1-2 immature trainee otters. The socio-economic conditions and livelihood status of the otter fishers` were found as not-satisfactory level whereas about 75% of total 36 fishermen were termed as very poor and they don`t have their own boat and nets for fishing. All of the surveyed fishers belong to the Hindu religion and less access to education, pure drinking water, and a healthy sanitation system. Due to scanty income, and resultant low-living standard, 14 otter fishers were found changed their ancient profession. Therefore, direct interventions are essential to support improved and sustainable socio-economic condition of the otter fishing community.
 Res. Agric., Livest. Fish.8(2): 249-257, August 2021

RASGRF2 gene fusions identified in a variety of melanocytic lesions with distinct morphological features

The WHO classification identifies nine classes of melanocytic proliferations according to location, UV exposure, histological, and genetic features. Only a minority of lesions remain unclassified. We describe five cases that harbored either an ERBIN-RASGRF2 or an ATP2B4-RASGRF2 in-frame fusion transcript. These lesions were collected from different studies, unified only by the lack of identifiable known mutations, with a highly variable phenotype. One case was a large abdominal congenital nevus, three were slowly growing pigmented nodules, and the last was an ulcerated nodule arising on the site of a preexisting small nevus, known since childhood. The latter was diagnosed as a 4mm thick melanoma with loss of BAP1 expression. The four other cases were compound, melanocytic proliferations with an unusual deep pattern of small dense nests of bland melanocytes encased in a fibrous background. The RASGRF2 fusion was confirmed by a break-apart FISH technique. Array CGH performed in three cases found non-recurrent secondary copy number alterations. Follow-up was uneventful. In silico analysis identified a single RASGRF2 fusion in the TCGA pan-cancer database, whereas RASGRF2 variants were stochastically distributed in all cancer subtypes.

Intensive exploitation of marine crabs and sea urchins during the middle holocene in the eastern Arabian peninsula offers new perspectives on ancient maritime adaptations

Maritime adaptation is a key component of the Neolithization process in Eastern Arabia. It is expressed by the development of diversified fishing techniques, the exploitation of hard marine animal materials (e.g., seashells, shark teeth, stingray's barbs, etc.) for both tools and personal adornments production, advanced seafaring, and colonization of offshore islands. Although a diet based mainly on the consumption of marine fish and mollusks, the importance of other seafood has been greatly underestimated in previous zooarchaeological studies. Large quantities of marine crabs (NISP = 10,619) and sea urchins (NISP = 2454) have been retrieved from newly excavated Neolithic sites in the United Arab Emirates. These data highlight local developments of interest for specific seafood and their intensive exploitation over several centuries of human occupation. This study focuses on methods for identifying the main edible marine crab and sea urchin species retrieved from archaeological sites in Eastern Arabia. Results from the Neolithic sites of Delma Island and the Umm al-Quwain lagoon are discussed.

Application of the FISH Technique to Visualize Sex Chromosomes in Domestic Cat Spermatozoa.

Simple SummaryThe study was conducted with the aim of visualizing sex chromosomes in domestic cat sperm. Our research was carried out using fluorescence in situ hybridization (FISH) technique and the microscopic analysis showed the presence of X and Y chromosomes in domestic cat spermatozoa. The procedure used for sperm decondensation and FISH is adequate to visualize chromosomes in domestic cat sperm.Fluorescence in situ hybridization is a molecular cytogenetics technique that enables the visualization of chromosomes in cells via fluorescently labeled molecular probes specific to selected chromosomes. Despite difficulties in carrying out the FISH technique on sperm, related to the need for proper nuclear chromatin decondensation, this technique has already been used to visualize chromosomes in human, mouse, cattle, swine, horse, and dog spermatozoa. Until now, FISH has not been performed on domestic cat sperm; therefore, the aim of this study was to visualize sex chromosomes in domestic cat sperm. The results showed the presence of X and Y chromosomes in feline spermatozoa. The procedure used for sperm decondensation and fluorescence in situ hybridization was adequate to visualize chromosomes in domestic cat spermatozoa and, in the future, it may be used to determine the degree of chromosomal abnormalities in these gametes.

Hypodiploidy in a pediatric patient of T-cell acute lymphoblastic leukemia: a case report

BackgroundT-cell acute lymphoblastic leukemia is a subtype of acute lymphoblastic leukemia, one of the most common childhood neoplasms. Hypodiploidy is a chromosome abnormality with fewer than 45 chromosomes and is associated with unsatisfactory clinical outcomes in acute lymphoblastic leukemia.Case presentationWe report clinical and genetic findings of a 14-year-old male with T-cell acute lymphoblastic leukemia with low-hypodiploidy. The medical history included neck pain for a month, facial nerve palsy on the right side for 6 days, fever, drowsiness, and weakness for 3 days, vomiting, diarrhea for 1 day. The physical examination presented features of hypovolemia, palsy of the facial nerve on the right side, enlarged lymph nodes, hepatosplenomegaly, sore throat, and petechiae of the skin. Radiological images indicated lesions of different organs. Bone marrow biopsy confirmed precursor T-ALL. In the FISH tests, KMT2A and BCR/ABL1 rearrangements were not observed. GTG banding revealed 3 cell clones, which confirmed the hypodiploidy. Multiplex RT-qPCR was performed. STIL/TAL1 (del1p32) gene rearrangement was found in the blast cells. Additional tests were performed using the CytoScan HD microarray technique. Molecular karyotype did not reveal hypodiploidy, but identified other abnormalities such as duplication of chromosomal regions: 4q25q35.2, 6p23.3p11.1 and 8p23.3q24.21, and the loss of heterozygosity of short arm chromosome 9. In two regions of the chromosome biallelic deletions were found at 9p21.3, including the CDKN2A, CDKN2B, IFNA1, MTAP genes and at 10q23.31, containing PTEN. The child died 9 days after diagnosis.ConclusionsBone marrow biopsy, GTG banding, FISH techniques, and molecular karyotyping were used to make an accurate diagnosis. This case documents a rapid progression of the disease and unfavorable results of T-cell acute lymphoblastic leukemia with hypodiploidy.

Over-Expression of ERG Predicts Poor Outcome in Acute Myeloid Leukemia

Introduction: Acute myeloid leukemia (AML) treatment aims at the eradication of all leukemic cells to achieve cure. Available treatments produce complete remission (CR) in up-to 80% of patients. However, ~60% of them will relapse. Various prognostic factors such as baseline white blood cell count (WBC), cytogenetics and mutations of FLT3 , NPM1 , CEBPA have been shown to affect the survival. The high expression of brain and acute leukemia cytoplasmic (BAALC) and ETS- related gene (ERG) has been associated with poor prognosis but due to limited prospective studies, their role as prognostic factors is still unclear. We aim to substantiate the prognostic value of BAALC and ERG expression in adult AML patients.Materials and methods: All patients included in this prospective study (N=149) between March 2012 and February 2015 underwent marrow for following investigations: (i) Cytogenetic analyses- by standard techniques of chromosome banding and FISH (ii) Mutation profiling of NPM1 , FLT3 -ITD and CEBPA by capillary electrophoresis and direct DNA sequencing. Long range PCR was done to detect KMT2A-PTD (MLL -PTD) (iii) BAALC and ERG expressions by quantitative real time PCR assays. Abelson (ABL ) gene was used as an internal control. According to the baseline median values of BAALC and ERG expression, patients were divided into high and low expressers.Patients received standard induction chemotherapy with daunorubicin 60 mg/m2 for 3 days and cytosine arabinoside 100 mg/m2 for 7 days. Marrow was done 21-28 days after start of chemotherapy. If marrow was in remission, then patients received 3 courses of consolidation therapy with 12-18 gm/m2 of cytosine arabinoside (HiDAC). Patients underwent allogeneic transplant if feasible according to molecular and cytogenetic risk.Statistical analysis was done using SPSS-21. Overall survival (OS) was defined as time from start of induction therapy to time to last follow up or death. Relapse free survival (RFS) was defined as time from achieving CR to time to relapse, death or last follow up if in CR. Results of the expression studies, cytogenetic and molecular groups were analyzed for their impact on OS and RFS. Variables known to have prognostic implications such as baseline WBC, cytogenetics risk groups and molecular markers were grouped according to high/low BAALC and ERG expressers. Comparison of these prognostic factors within high/low expressers was carried out by Chi-square method. Survival was calculated by Kaplan-Meier method and prognostic factors were compared by log-rank test. Multivariate analysis was carried out using the Cox proportional hazards model. All covariates whose univariate models reflected a P value less than 0.2 were considered for inclusion in the model.Results: A total of 149 patients were accrued. The median age of the cohort was 27 years (range 15-58 ) with male predominance (M:F =98:51). Of 149 patients, 105 achieved CR after 1 or 2 cycles of chemotherapy. Twenty-seven patients were refractory of which 18 were lost to follow up and hence excluded from OS analysis. Seventeen patients died during induction. The OS of 131 patients was 36.5% at 2 years. The OS and RFS of 105 patients who achieved CR was 54% and 43.8% respectively. The median value (60 BAALC copies /ABL and 58 ERG copies /ABL ) was used to distinguish high expressers from low expressers. At baseline, copy numbers of 149 patients ranged from 11.58 to 242.23 for BAALC and 16.2 to 328.2 for ERG. For BAALC , 69/149(46.3%) were high expressers as compared to 80/149 (53.7%) as low expressers. Concerning ERG , 76/149(51%) were high and 73/149(49%) were low expressers. The OS and RFS of high BAALC versus low BAALC expressers at 2 years was 13.8% vs 59.8% (p<0001) and 17.6% vs 72.1% (p<0001) respectively. Similarly OS and RFS of high ERG vs low ERG expressers at 2 years was 5.3% vs 66.4% (p<0001) and 5% vs 71.2% (p<0001) respectively (Figure).The median baseline WBC count was significantly higher in high BAALC/ERG expressers. There was no difference in distribution of FLT3 -ITD, NPM1, CEBPA, MLL -PTD and cytogenetic risk groups in high versus low BAALC and ERG expressers. Multivariate analysis showed that ERG overexpression was only prognostic factor affecting OS and RFS compared to high BAALC expressers, MLL -PTD mutation, cytogenetic risk groups and baseline WBC.Conclusion: This study shows that high ERG expression adversely affects prognosis of AML patients independent of other well known prognostic factors [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Incidences of Submicroscopic Deletions Are Variable According to Disease Entities and Chromosomal Translocations in Hematologic Malignancies: Investigation by FISH.

Submicroscopic deletions of gene in recurrent chromosomal rearrangement are known to occur frequently in hematologic malignanacies. With wide application of FISH technique in diagnosis of hematologic malignanices, it has become easy to assess the submicroscopic deletions. We investigated the incidence of submicroscopic deletion and analyzed their association with specific genetic rearrangements in various hematologic malignancies. FISH study was conducted with bone marrow cells in 336 patients with acute lymphoblastic leukemia (ALL), 223 patients with acute myeloid leukemia (AML) and 103 patients with chronic myelogenous leukemia (CML). We performed extra signal (ES)-FISH BCR/ABL, ES-FISH TEL/AML1 rearrangement and dual color split MLL rearrangement for ALL and Dual fusion-FISH (D-FISH) AML1/ETO, D-FISH PML/RARA and dual color break apart-MLL rearrangement for AML. For CML, D-FISH BCR/ABL were done. The incidence of submicroscopic deletion in the patients with chromosomal rearrangement was highest in TEL/AML1 rearrangement (65.0%), followed by BCR/ABL (10.9%), MLL (5.6%), AML1/ETO (4.0%), and PML/RARA (0.0%). Fifteen (19.0%) of 79 patients with CML showed either BCR and/or ABL deletion on derivative chromosome 9. One (5.6%) of 18 patients with MLL+ acute leukemia (5 ALL, 13 AML) showed submicroscopic deletion of telomeric portion of MLL gene. One (4.0%) of 25 patients with AML/ETO+ AML showed deletion of AML1 gene on derivative chromosome 21. None (0%) of 22 patients with PML/RARA+ AML and 59 patients with BCR/ABL+ ALL showed deletion in chromosomal rearrangement. Of note, none of 59 patients with BCR/ABL+ ALL (including major and minor rearrangement) showed submicroscopic deletion, in contrast to that of patients with BCR/ABL+ CML. In conclusion, the incidences of submicroscopic deletion was quite different among specific genetic changes and disease entities. Careful FISH study should be included in the work-up for hematologic malignancies, and their association with clinical prognosis need to be further studied.

Customized Solutions for Coiled Tubing Interventions in the Bolivian Sub-Andean Basin

This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper SPE 202620, “A Review of 25 Coiled Tubing Well Interventions: Customized Solutions for Bolivian Sub-Andean Basin,” by Jovanny A. Hernandez, SPE, Luis F. Antelo, SPE, and Carlos D. Rodriguez, Halliburton, et al., prepared for the 2020 Abu Dhabi International Petroleum Exhibition and Conference, Abu Dhabi, held virtually 9–12 November. The paper has not been peer reviewed. Fields in the Bolivian Sub-Andean Basin are remote and difficult to access. The producing zones include the country’s most challenging wells, with depths of up to 26,000 ft, with high pressure/high temperature (HP/HT), high gas cut, crossflow, dogleg severity, and well-access restrictions. The complete paper reviews 25 coiled tubing rigless well interventions (CTRWI) to extend the life of those wells, including operations involving nitrogen (N2) lift, acid wash, milling, shifting sleeves, setting packers, stimulation, velocity strings (VS), and fishing. Introduction CTRWI in Sub-Andean Basin fields had not been implemented historically because of limited road access to the fields, lack of available equipment with high technical capabilities, high pressure, and well depth. Beginning in 2017, however, operators evaluated the risk and elected to perform CTRWI involving stimulation, cleanout, N2 lift, fishing, VS jobs, and other techniques. Equipment with specialized capabilities was requested to address the operational requirements and the ability to travel on the remote roads while respecting transit regulations limiting maximum weight to 55 tons. The challenges to transporting equipment economically include - Transportation of large reels of 2⅞-in. coiled tubing (CT) string to complete dual-sectioned VS installations - Transportation of CT unit with 6,600 m of 1¾-in. CT string (weight of less than 55 tons) - Continuously moving large volumes of N2 to the field Wells in these fields were drilled no more than 10 years ago. The majority were built with smart completions, several production layers separated with swell packers and flowing through sliding sleeves configured with the same direction of actuation for opening and closure. Completions are configured with production tubing sizes of 7, 5, 4½, and 3 in. The tubing and accessories are made from chrome 13 because of the presence of carbon dioxide in the production fluids. The region includes some exploratory fields having HP/HT conditions and mature fields with declining production. These wells are important for both the operators and the local government because their production represents more than 50% of national production. On-Site Laboratory Testing Characteristics of produced formation water and mineralogy tests of water samples helped identify a calcium carbonate (CaCO3) scale type. Because CaCO3 scale is known to be acid-soluble, a tailored acid-treatment system was selected with a static formation temperature between 220 to 286°F. On-site laboratory tests using a combination of 13% acetic and 9% formic retarded acid treatment systems were applied to the samples obtained, and results of a solubility test were observed. The selected treatment was demonstrated to be highly effective at dissolving CaCO3 scale according to the test made at the wellsite. High confidence was placed in the test results of the acid-treatment sample because dissolution was above 85% in a 4-hour test period under static well temperature.

TP53 Abnormalities and MMR Preservation in 5 Cases of Proliferating Trichilemmal Tumours.

Proliferating trichilemmal tumours (PTT) are defined by a benign squamous cell proliferation inside a trichilemmal cystic (TC) cavity. A possible explanation of this proliferative phenomenon within the cyst may be molecular alterations in genes associated to cell proliferation, which can be induced by ultraviolet radiation. Among other genes, alterations on TP53 and DNA mismatch repair proteins (MMR) may be involved in the cellular proliferation observed in PTT. Based on this assumption, but also taking into account the close relationship between the sebaceous ducts and the external root sheath where TC develop, a MMR, a p53 expression assessment and a TP53 study were performed in a series of 5 PTT cases, including a giant one. We failed to demonstrate a MMR disorder on studied PTT, but we agree with previous results suggesting increased p53 expression in these tumours, particularly in proliferative areas. TP53 alteration was confirmed with FISH technique, demonstrating TP53 deletion in most cells.

Nutrient Deficiency Promotes the Entry of Helicobacter pylori Cells into Candida Yeast Cells.

Simple SummaryHelicobacter pylori is a pathogenic bacterium which causes several gastric and extra-gastric pathologies in humans. This pathogen is capable of entering eukaryotic cells of humans or of other species, including yeasts of the genus Candida. These yeasts are resistant to stressing environmental conditions (such as pH changes or scarce nutrients) which threaten the viability of H. pylori. Therefore, Candida yeasts may harbor this bacterium when subjected to stressing conditions or become transmission vehicles for it. Further research is required to establish the stressing environmental factors triggering the harboring of H. pylori within yeasts. The present work evaluated if deficiency or absence of the necessary nutrients favors the endosymbiotic relationship between these two microorganisms, facilitating the viability of the bacterium. In fact, a deficiency of nutrients increased the harboring of viable H. pylori cells within the yeast cells. On the contrary, in the complete absence of nutrients, the presence of intra-yeast bacteria was reduced. Therefore, yeast cells may contribute to the subsistence of this pathogenic bacterium when subjected to nutrient deficiency until it may infect an appropriate host, such as humans. The present work may also contribute, with further studies, to elucidate the transmission routes used by the pathogen H. pylori to infect its hosts.Helicobacter pylori, a Gram-negative bacterium, has as a natural niche the human gastric epithelium. This pathogen has been reported to enter into Candida yeast cells; however, factors triggering this endosymbiotic relationship remain unknown. The aim of this work was to evaluate in vitro if variations in nutrient concentration in the cultured medium trigger the internalization of H. pylori within Candida cells. We used H. pylori–Candida co-cultures in Brucella broth supplemented with 1%, 5% or 20% fetal bovine serum or in saline solution. Intra-yeast bacteria-like bodies (BLBs) were observed using optical microscopy, while intra-yeast BLBs were identified as H. pylori using FISH and PCR techniques. Intra-yeast H. pylori (BLBs) viability was confirmed using the LIVE/DEAD BacLight Bacterial Viability kit. Intra-yeast H. pylori was present in all combinations of bacteria–yeast strains co-cultured. However, the percentages of yeast cells harboring bacteria (Y-BLBs) varied according to nutrient concentrations and also were strain-dependent. In conclusion, reduced nutrients stresses H. pylori, promoting its entry into Candida cells. The starvation of both H. pylori and Candida strains reduced the percentages of Y-BLBs, suggesting that starving yeast cells may be less capable of harboring stressed H. pylori cells. Moreover, the endosymbiotic relationship between H. pylori and Candida is dependent on the strains co-cultured.

Ossifying low grade endometrial stromal sarcoma with PHF1-BRD8 fusion

Low-grade endometrial stromal sarcoma and ossifying fibromyxoid tumors are two types of mesenchymal tumors that share no similarities in terms of site, sex, and morphological characteristics. They are rare, low grade tumors of uncertain lineage, with no definite immunological markers. Interestingly, a common PHF1 gene- related rearrangement was observed in these two tumors. Here, we report a case of endometrial stromal sarcoma with distinct ossification. Microscopically, the tumor is composed of bland-looking ovoid cells with low cellularity in the fibromyxoid stroma. Foci of metaplastic bone formation were noted. Using a combination of FISH, transcriptome sequencing, and molecular techniques, we identified a new PHF1-BRD8 fusion transcript, which was previously described, but in its reciprocal fusion form. This case expands the current understanding of low-grade endometrial stromal sarcoma and emphasizes the importance of molecular characterization of unique fusion, which may be related to its distinct morphological features and the possibly chemosensitive target.

Fish Ecology of the Alto Madre de Dios River Basin (Peru): Notes on Electrofishing Surveys, Elevation, Palm Swamp and Headwater Fishes

Our study analyzes the distribution of fish communities related to the environmental variables of the Alto Madre de Dios River, an Andean-Amazon watershed of southern Peru, between 300 and 2811 m a.s.l. within the Manu Biosphere Reserve. We provide new ecological and diversity data on fishes for these poorly studied rivers and new data for palm swamp habitats. With electric fishing techniques, we collected a total of 1934 fish specimens belonging to 78 species, 42 genera and 15 families. To assess main patterns of diversity we combined SIMPER and ANOSIM with canonical correspondence analysis to obtain an overview of the community structure of fish and their distribution related to aquatic habitats. Our results show an important shift on fish diversity at 700 m a.s.l. separating headwater and middle-lowland communities. Electrofishing was a hindrance due to the depth, flow and low conductivity of the rivers, but also allowed us to capture fish not observed with other techniques. We also compared the use of elevation with slope as an alternative variable for statistical analysis. Our results show that slope offers a solid and equivalent explanation for fish distribution variability, avoids redundance, and instead of giving geographical data offers ecologically solid information.