GENEWS December 2022 Issue

GeneSoc conquers first hybrid Genetics Week

by CHRISTIAN VELASCO (Reprimo)

TheUPLB Genetics Society (GeneSoc) celebrates the annual Genetics Week with this year’s theme: “The Missing Link: Binding Genetics and Law to Investigate Unresolved Mysteries”. The organization held a hybrid of virtual and face-to-face events from November 26 to December 2, 2022. Face-to-face events, including the posting of the physical exhibit, were held at the Wing C, Institute of Biological Sciences at the University of the Philippines - Los Banos.

To commence Genetics Week, a webinar was conducted last November 26 with the theme: “Forensic Science: The Role of Genetics in Solving Mystery Investigations” via Zoom. Dr. Maria Corazon De Ungria, who is an honorary member of the organization, served as the lecture speaker. She is currently the head of the DNA Analysis Laboratory of the National Science Research Institute at the University of the Philippines Diliman (UP-DAL) and the director of the Program on Biodiversity, Ethnicity, and Forensics at the Philippine Genome Center (PGC). Dr. De Ungria expounded on the power of DNA as a tool for identification and profiling, and how

it provides objective evidence that unveils cases with the help of molecular technology. She emphasized the challenges of forensic science in the country such as the lack of a national criminal DNA database, the high cost of DNA testing, the insufficient compliance with standards on the collection of biological samples, among others. Dr. De Ungria supported the passing of laws that would provide awareness and advancement to forensic science and allocating funds that would strengthen the country’s forensic technology in solving a variety of cases.

GeneSoc also posted a physical exhibit at Wing C, IBS which features posters and illustrations that showcase the principles and applications of

forensics genetics. Other relevant topics include nextgeneration sequencing technology (NGS), forensic genetic genealogy, and the genetics of criminal behavior which can be found in the exhibit. Aside from the webinar and exhibit, GeneSoc also opened a major application process for prospective applicants or “geneterns.” It is a week-long process that evaluated the geneterns’ determination to join the organization and their interest and

passion for genetics. GeneSoc, with its goal of increasing awareness about the science of genetics in the country, released the December 2022 Issue of its official publication GENEWS on the first day of December both at the physical exhibit and online at Blogspot and Issu.

The successful celebration of Genetics Week would not be possible without the dedication and support of the organization’s resident members, the Genes.

GeneSoc spearheads first F2F BIO 30 Tutorials since the pandemic

by FRANCISCO ESCALA III (Reprimo)

answers. Apart from handouts, free snacks were also given for the two-hour long tutorials.

Prof. Alcabedos was awarded a certificate of appreciation and a token of gratitude for her time and expertise. At the end of the session, evaluation sheets were distributed to

the students.

In addition to two BIO 30 Tutorials that will be given during this first semester, the Genequiry Discord server of The UPLB Genetics Society will remain open to entertain any genetics-related questions from students currently taking BIO 30.

After two years of conducting online BIO 30 Tutorials amidst the pandemic, The UPLB Genetics Society together with The UPLB Learning Resource Center resumed a face-to-face setup of the said tutorials last October 10, 2022 from 7:00 PM to 9:00 PM in the Makiling Ballroom Hall at the Student Union Building, UPLB.

The BIO 30 tutorials aim to help students in reviewing for their first long exam in BIO 30: Introductory Genetics. Professor Riaflor Alcabedos from the Genetics and Molecular Biology Division of the Institute of Biological Sciences (IBS-GMBD) served as the instructor

during the tutorials wherein she summarized and synthesized Lessons 1 to 4 of the BIO 30 curriculum.

Mock exam handouts were also given to the students in which they simultaneously answer the questions and Prof. Alcabedos explains the

GeneSoc alumni, honorary members grab awards at 44th ASM

by KOOZAE UMALI (Hachimoji)

alumni and honorary members were recognized at the 2022 Annual Recognition of Outstanding Scientific Achievements of the National Academy of Science and Technology Philippines (NAST PHL), during their 44th Annual Scientific Meeting (ASM).

GeneSoc

The 2022 Outstanding Scientific Paper Award (OSPA) was awarded on two of the papers co-authored by GeneSoc alumni and honorary members. Asst. Prof. Jickerson P. Lado (Integrons), Dr. Maria Genaleen Q. Diaz (F1), GeneSoc Honorary Member Dr. Rita P. Laude, along

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GeneSoc alumni, honorary members grab awards at 44th ASM

with their coauthors were recognized for their paper entitled "Transcriptome Analysis of ‘Philippine Lono Tall’ Coconut (Cocos nucifera L.) Endosperm Reveals Differential Expression of

Genes Involved in Oil Biosynthesis." which was published on the 102nd volume (Coconut Genomics Special Issue) of the Philippine Agricultural Scientist last 2019.

Moreover, Lado, Diaz, and Laude, together with Beatriz Z. Arellano,

MD (Riboprobes), and other coauthors were also recognized for their work entitled Early Differential Expression of Galactomannan Biosynthesis Genes in 'Makapuno' Coconut (Cocos nucifera L.) Revealed by the De Novo Assembly

and Analysis of Endosperm Transcriptome, which was published in the same issue of the Philippine Agricultural Scientist.

OSPA is given for papers published in Clarivate Analytics or Scopus-listed journals in the PH, within 5 years preceding the year of the award. Papers are judged based on the criteria of content quality and originality, contribution to S&T, clarity of presentation, and thoroughness of the

GeneSoc alum, NAST PHL academician receives 2022 UPAA AchievementDistinguished Award in Science and Technology

by ALLEN MALABAYABAS (Reprimo)

documentation. Meanwhile, GeneSoc alumnus and Asst. Prof. Jae Joseph Russell B. Rodriguez (Ribozymes) clinches third place on the 2022 National Academy of Science and Technology Talent Search for Young Scientist (NTSYS).

Rodriguez presented his study entitled “An Integrated System for Forensic DNA Testing of Sexual Assault Cases in the Philippines” as a finalist on the virtual paper presentation of the 2022 NTSYS held last April 11, via Zoom.

Academician

Glenn B. Gregorio of the National Academy of Science and Technology Philippines (NAST-PHL) was hailed as a recipient of the 2022 UPAA Distinguished Achievement Award in Science and Technology (Agriculture-Plant Breeding and Stress Tolerance).

On October 10, during their 109th year, The University of the Philippines Alumni Association (UPAA) recognized Dr. Gregorio’s valuable

contributions to genetics and breeding for his work on rice salinity tolerance and related abiotic stresses.

In about three decades of his dedicated

career at the International Rice Research Institute (IRRI), Dr. Gregorio specialized in plant breeding focusing on rice tolerance to saline-prone and problematic soils.

carried out rapid screening techniques that aided in the fast-tracked identification and development of salt-tolerant germplasm and breeding lines.

GeneSoc alumni recognized at 104th UPLB Loyalty Day

by GEROMN DACQUIL (Reprimo)

October 10, 2022, the University of the Philip pines - Los Baños (UPLB) celebrated its 104th UPLB Loyalty Day and Alumni Homecoming wherein two GeneSoc alumni received accolades – Dr. Mark Kristof fer U. Pasayan (Batch Anlage) and Dr. Glenn B. Gregorio (Batch Recombinants).

Last

This year's Loy alty Day theme is "Strengthening the Partnership between UPLB and Alumni for more Progressive Communities."

Dr. Pasayan received the CAS Distinguished Alumni Award for Public Health Promotion. Currently, he is known as an infectious dis ease specialist. Meanwhile, Dr.

Gregorio and his family received the 2022 UPLBAA Multi-generation UPLB Alumni Family Award. This award is given to families who have pro duced three or more successive generations of UPLB alumni.

With these ex emplary achieve ments, The UPLB Genetics Society congratulates Dr. Mark and Dr.

Glenn and his family.

UPLB celebrates the Loyalty Day and Alumni Homecoming ev ery year to com memorate the heroism of the young men and women of the UP College of Agri culture (UPCA) who took the op portunity to serve in the Philippine National Guard during World War I back in 1918.

These are now being adopted by various research institutions in the Philippines and other countries around the globe, in their efforts to develop climate change-ready rice varieties.

The distinguished Dr. Gregorio recently conferred the Academician rank as a NAST-

PHL member in 2018. Other prestigious recognitions that Dr. Gregorio received are: Ten Outstanding Youth Scientists of the Philippines (TOYS) (1980); Outstanding Young Scientist (OYS) in the field of Genetics (2004); Crop Science Society

of the Philippines Achievement Award for Crop Science Research (2004); Honorary Foreign Scientist Award at the Rural Development Administration (RDA) of Korea (2002-2005); The Outstanding Young Men (TOYM) of the Philippines (2004); Ho Chi

Minh Medal for "Having Great Contribution to the cause of Agriculture and Rural Development of Vietnam" (2012); Crop Science Society of the Philippines Achievement Award in Research Management (2014), and the Honorary Fellow

of the same Society (2019).

The UPAA Distinguished Achievement Alumni Award is given to distinguished UP alumni for their outstanding achievements that bring honor and recognition to their Alma Mater and to the country.

GeneSoc alumnus, NAST PHL academician receives 2022 UPAA Distinguished Achievement Award in Science and Technology

Svante Paabo wins Medicine Nobel Prize for his work in paleogenomics

DNA sequencing links aged hair shafts to the last imperial rulers of Russia

Forensic genetics unveils Brazil’s “Robbery of the Century”

Svante Paabo wins Medicine Nobel Prize for his work in paleogenomics

by MARK MERCADO (Reprimo)

The Nobel Prize is a legacy of Alfred Nobel to those who impart the "greatest benefit to humankind" (Nobel Prize Outreach, n.d.) in the fields of Chemistry, Physics, Physiology or Medicine, Peace, and Literature.

This year, the Nobel Prize in Medicine or Physiology was conferred to Svante Paabo for his discoveries and work on the genomes of extinct hominins and their link to human evolution. Svantee Paabo is a Swedish evolutionary geneticist and one of the founders of paleogenetics. One of the pioneering research that he has done in paleogenetics was the sequencing of the genome of Neanderthal, an extinct species and relative of Homo sapiens. Apart from that, he also made a sensational discovery of another extinct hominin, the Denisovan. He is currently teaching molecular evolutionary biology in Leipzig University.

Sequencing the human genome proved to be a monumental task for

humanity. More seemingly impossible was the sequencing of extinct hominin genomes – yet it was accomplished by the research led by Svante Paabo. Through his analysis in paleogenetics, it wasX discovered that the said extinct hominins had undergone a gene transfer to the Homo sapiens aligned with the migration event in Africa, 70 000 years ago. As such, the gene flow from extinct hominins also influenced the physiology of modern humans. The discovery of the contributions and differences of the extinct Neanderthal and Denisovan genomes to the modern human genome would have a profound implication on medicine and genetics. For example, people with the version of gene

EPAS1 from Denisova have advantages in high altitude environments. This gene is common in Tibetans. Moreover, the geospatial distribution of genes was also elucidated which depended on their location and evolutionary history.

During the start of Paabo’s career, he already had a vision of using the modern genetic method in studying archeological remains. But throughout his research, he encountered challenges such as the chemical modification and degradation of the DNA samples, and even contamination from bacteria and humans who managed the samples. In 1990, he continued working on archaic DNA by analyzing the genetic material in the minute mitochondria of the Neanderthal since it is present in many copies. Thus, this increased the likelihood of proper

sequencing of the mitochondrial genome.

Neanderthals have been found to be genetically different from the results of the comparisons between modern humans and chimpanzees. But these could only give us limited information, so after sequencing the mitochondrial genome, Paabo took the task to another level - sequencing the nuclear genome. As he was given the opportunity to set up the new Max Planck Institute, Paabo made it possible by improving the methods to isolate and analyze the DNA and incorporating the technical developments in sequencing technology. He also sought participation of several critical collaborators who were experts in the field of population genetics and advanced sequence analysis. Finally, in 2010, they published the draft sequence for the Neanderthal genome. The results of comparative analysis from dental evolution showed that the Neanderthals and Homo sapiens diverged, and that their recent common ancestor lived 800,000 years ago.

Through his scientific efforts and intensive research, a new field of scientific discipline has emerged – paleogenomics. Paleogenomics aims to study and reconstruct the genomic imprint of samples from fossils and remains of ancient organisms, along with the genetic changes that happened throughout evolution. This could deepen the understanding on how our own species (Homo sapiens) migrated in the past and evolved relative to other Hominins.

© Frank Vinkein | Max Institute for Evolutionary Anthropology

DNA sequencing links aged hair shafts to the

last imperial rulers of

by NIKKI MATTA (Helraiser)

History has its eyes on important figures, and without a doubt, the Romanov Family is not an exception. The end of the Romanov dynasty sparked a new chapter not only to Russia but also, to the world. The Russian Revolution of 1917 introduced the communist and socialist ideas that eventually formed a new economic system known as Socialism, where different countries followed through.

The key players to the end of the Romanov dynasty were the Bolshevik revolutionaries. Various accounts and reports reveal that the Romanov family were held prisoners and executed in July 1918. After execution, the fallen bodies were quickly buried in a “superficial and hastily dug” pit around the execution site. Due to the turmoil brought about by the sudden changes in the political and social climate in Russia, it

was only in 1991 that the first skeletons of the Romanovs were recovered. The recovery of skeletons from the execution site was temporarily identified to be of the Romanov family, in particular, the Tsar, Tsarina, three of five children of the royal family, and four family retainers. The bodies were subjected to DNA testing using mitochondrial DNA analysis, and the identity was confirmed to be members of the Romanov family after

Russia

Photographs taken from three different hairs that were found in the Fabergé locket. (A) Magnification 100×. (B) Magnification 200× shows that the proximal end of the hair appears cut. (C) Magnification 200× shows that the proximal end of the hair appears broken.

comparing the DNA profile of the remains to the DNA profile of Prince Philip, Duke of Edinburgh, who is a living grandnephew of Tsarina at that time. In the succeeding years, more recoveries were made, and consequently, identities were determined and confirmed through the integration of anthropological, mitochondrial, and nuclear DNA analyses. One of the most recent recoveries related to the Romanov family came from Loreille et al.’s study published in January 2022. In their study, they subjected the hair shafts found from the artifacts associated with the Romanov family to an improved DNA Extraction protocol and Illumina sequencing, a type of Next-Generation Sequencing (NGS) technique. The latest

artifacts from the study was a Karl Fabregé pendant and a framed photograph of Queen Louise of Hesse-Kassel. The Karl Fabregé pendant contained a photograph of the Empress Alexandra Feodorovna Romanov and a lock of lightcolored hairs assumed to be from the Empress. The framed photograph of Queen Louise also contained locks of light hair in between the glass of the frame and the photograph itself. These available samples from the artifacts were the ones analyzed to confirm if the hairs belong to a member of the Romanov family. However, studies have also reported on the challenge of using aged and degraded samples for mtDNA analyses. For example, one study has established that

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Image source: thetravel.com

the likelihood to obtain hypervariable regions for mtDNA profile decreases from 90% to almost only 60% when a hair sample is aged around 0-6 years old and when the sample is greater than 20 years old, respectively. Additionally, another paper reports that the average mtDNA that can be collected in human hair samples that are aged at 50-100 years old is only around 61 bp. So, an increased sample age means an increased difficulty to obtain DNA information that may be useful for further analyses.

Loreille and colleagues used Next-Generation Sequencing to develop DNA data from the DNA samples present in the recently-obtained Romanov family artifacts. In order to maximize the DNA extraction in these aged samples, their team developed a modified protocol for the extraction. The hair samples were handled in a laboratory for low-quality and low-quantity DNA samples, with limited access to personnel. In handling the samples, they ensured that the personnel wore Personal Protective Equipment with singleuse garments and goggles. Double-gloving was also required during handling. The reagents used for the process were all irradiated before they were introduced to the samples, as well as the plastic consumables so that the risk of contamination would

be minimized. The modified DNA extraction protocol is as follows: the sample (aged rootless hair shaft) is decontaminated by using a detergent (5% Terg-a-zyme solution) and was subjected to sonication. After decontamination, lysis/digestion of the samples were carried out by using digestion buffer and proteinase

main modification in the protocol is the magnetic bead-based purification applied to the singlehair samples since the silica-based purification is the common protocol for the process. DNA is then quantified using fluorometric methods with addition of the determination of dsDNA through dsDNA high sensitivity assay kit. The DNA library

small mtGenome of the samples.

Both the hair samples obtained from the pendant and the framed photograph produced mitochondrial and nuclear DNA results. In addition, the biological sex of the sample source was also determined. Relatedness estimates were only available for the hair samples obtained from the pendant because the nuclear reads of the hairs obtained from the framed photograph were insufficient for a successful assessment.

K, with addition of irradiation in a crosslinker. The samples were then incubated in a thermomixer so they may be fully digested. Two purification methods were applied: a silica-based method and a magnetic bead-based purification. The silicabased was applied to the multiple-hairs sample, while the magnetic bead-based was for the single-hair sample. The

was prepared using the NEBNext Ultra II DNA library prep kit. There is a step for hybridization capture so that the mitochondrial DNA may be enriched through amplification and purification with AMPure XP beads. The quantification from this step was done through Qubit Fluorometer, and a NGS kit, the MiSeq FGx Sequencing System, was used to sequence the

The hairs from the pendant revealed a mitochondrial genome profile that is similar to the haplogroup of Empress Alexandra’s maternal lineage, which is publicly available in GenBank. The Nuclear DNA information of the samples from the pendant was derived from the shotgun sequence library, and it was confirmed that the hair samples was a human DNA with 98.9% belonging to the nuclear genome. Using the shotgun sequence library, the biological sex of the sample source was also determined, and the Rx confidence interval revealed that the sex for the sample source is a female, therefore eliminating that the possible source of the sample is from the Romanov son, Tsarevich Alexis. Finally, the relatedness estimates for the hair sample in the pendant showed allele mismatch proportions that reveal that the samples come from one source, which

Picture of Queen Louise of Hesse-Kassel after restoration. Courtesy of M. Perekrestov, from the Russian History Foundation.

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is a single individual only. For the hair samples obtained from the framed photograph, the mitochondrial DNA results showed a haplogroup profile similar to the publicly available sequence of Tsar Nicholas Romanov. There is a noticeable inconsistency due to a presence of a point heteroplasmy from the sequence of Tsar Nicholas, which cannot be pointed in the hair sample from the framed photograph since it produced homoplasmic points in the cytosine, and it was assumed that this may be from hydrolytic deamination, a common form of damage in ancient molecules. For the nuclear DNA data, only the read and DNA length was determined from the sample. These data were insufficient for relatedness analysis, but

the biological sex was still be determined from the results of the nuclear DNA, and so the confidence interval based on the nuclear DNA of the hair sample from the framed photograph revealed that the biological sex of the sample source is female, confirming the possibility that the hair is sourced from Queen Louise.

In conclusion, Loreille et al.’s work showed that minimal, aged, and degraded samples such as hairs may be used for forensic casework. This study shows that DNA information can be successfully obtained in samples with limited quantity because they may still produce considerable DNA information after extraction. Loreille et al.’s study highlights the importance of an improved protocol in

handling such types of samples. In addition to developing a protocol to extract and amplify DNA from limited, aged, and degraded samples, the methods and results of this study have substantial contributions for forensic casework especially for cases like missing persons where there is very limited sample availability, given that there are alternatives for familial reference information for identity-linking analyses.

The information presented on the Romanov Family case was derived from the scientific paper entitled "Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family", published under Genes which can be accessed at http://dx.doi. org/10.3390/genes13020202.

Forensic genetics unveils Brazil’s

“Robbery of the Century”

On April 24, 2017, a robbery occurred in a cash-transit facility in Ciudad del Este, Paraguay. A large group of heavily armed gangsters targeted the vault of Prosegur, a cash-protection service company, and stole cash amounting to more than $11.7 million. Due to the large-scale nature of the heist, the media later labeled it as the infamous “robbery of the century.”

by JAN DEQUITO (Informosomes)

Prior to the robbery, a group of bandits besieged the city and surrounded the company’s building with torched vehicles. Whilst the terrorizing of the city occurred, another group of gang members bombed the Prosegur office to break into the safe and steal millions of dollars. The assault lasted for around three hours which resulted in injuries sustained by one officer and three civilians, and even the death of one police officer.

The location of the crime, Ciudad del Este, sits at the intersection of Paraguay, Brazil, and Argentina. The existing Tripartite Command in the interstates formally enabled the collaboration between the police forces in the cities of Puerto Iguazu in Argentina, Foz do Iguaçu in Brazil, and Ciudad del Este in Paraguay

© Ministerio del Interior

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Forensic genetics unveil Brazil's

The investigation by the security forces pointed out that a notorious Brazilian criminal organization was behind the robbery. The large group of burglars scattered into smaller groups as they fled from the police. One group of suspects attempted to escape by crossing a lake towards Brazil, but they were intercepted by the Brazilian Federal Police. Other criminals resorted to kidnapping civilians, but they were later apprehended by police officers. In another confrontation during a chase, three of the fugitives were killed. Through the joint efforts of the security forces in different regions, several suspects were arrested and detained for interrogation. From the information gathered, the police were able to track down the "headquarters" of the criminals in Ciudad del Este. As requested by the Paraguayan

National Police, the Brazilian Federal Police handled the crime scene investigation and forensic analysis in the Prosegur case. They collected pieces of evidence at the Prosegur branch office, the "headquarters," and clashing sites with the aim of recovering biological traces that could generate genetic profiles to be used in criminal identification.

Among the materials collected are personal items found in the "headquarters," abandoned bags around the vicinity of clashing sites,

"Robbery of the Century"

and later, seized vehicles used by the burglars. All evidence found was sent to the DNA laboratory for sample analysis.

Brazil has an Integrated Network of DNA Database (RIBPG), wherein the genetic profiles of convicted offenders and suspects are stored as references for linking different crime scenes to aid in identifying the culprits involved. After gaining judicial authorization, the genetic profiles obtained from the Prosegur case were permitted to be inserted into the network.

However, as per protocol, a genetic profile must first meet the technical parameters for it to be included in the National DNA Database. An internal database was exclusively created for the Prosegur case so all genetic profiles obtained in the investigation could be compared to the reference profiles in the database.

Overall, there were 457 pieces of evidence retrieved in the investigation—a record-breaking number of materials ever received by the Brazilian forensic DNA laboratory until 2021. As the

case was a matter of urgency, DNA examinations had to be done in the shortest time possible. The laboratory team was divided into groups for the different tasks: a sampling team, a laboratory benchwork team to process DNA extraction to amplification, and a group of experts for analysis and report writing.

In a span of ten days since receiving the materials, 577 samples were obtained and analyzed. Substances such as saliva, blood, and semen were prioritized in the sampling because these have

© Gustavo Galeano | Getty Images

greater potential for yielding genetic profiles. The biological stains obtained were categorized into four major groups: wearer DNA, buccal epithelium/ saliva, "touch DNA,” and blood.

Only 240 samples, or less than half of the total, were amplifiable. This means other samples had insufficient DNA traces to generate genetic profiles. In the end, 138 out of 240 amplified samples were interpretable and eligible for comparison. The summary of the processed samples is illustrated in the

figure below.

The most common biological material extracted from all of the evidence was the wearer DNA. The next three were buccal epithelium or saliva, "touch DNA," and blood.

Apart from blood, the biological trace that yielded the greatest number of reportable genetic profiles of high quality was the buccal epithelium or salivary DNA. The buccal epithelium/ saliva traces were collected mainly from cigarette butts, cups, and bottles. Wearer DNA, which

is biological material shed in substrates such as clothing, balaclavas, and towels, was the next best biological trace. This was followed by "touch DNA," which was collected from objects handled by the robbers, such as tools and vehicles.

Through DNA examinations, it was revealed that at least 47 individuals participated in the crime, and their genetic profiles were entered into the database. It was revealed that 17 profiles from the Prosegur case matched with other profiles

from 21 unrelated crime scenes, which led to the identification of seven more individuals. Some of the burglars who participated in the Prosegur robbery turned out to be involved in other felonies in six Brazilian states between 2013 and 2020. The punishment for the perpetrators in the Prosegur robbery case includAed 26 to 34 years of imprisonment and a fine. The Prosegur case is another breakthrough that highlights the essence of forensic genetics. DNA profiling continues to

demonstrate its utility in the criminal justice system, as most of the evidence obtained in the investigation came from traces of DNA. Comparing stain profiles helped identify the culprits behind the robbery and even link their involvement to other criminal activities. The casework also sheds light on the effectiveness of having a DNA database to assist any type of criminal investigation. Aside from being dubbed the "robbery of the century" and being the biggest Brazilian forensic genetics case, the Prosegur case also won the DNA Hit of the Year in 2020.

Amplified samples (Source: da Silva Junior, et al. (2022). The “Robbery of the Century”: The biggest Brazilian forensic genetics case. Forensic Science International: Reports 5)

The information presented on the Prosegur case was derived from the case report entitled “The ‘Robbery of the Century’: the biggest Brazilian forensic genetics case”, published under Forensic Science International: Reports which can be accessed at https://www. sciencedirect.com/ science/article/ pii/S266591072 2000081

SUPER-RECOGNIZERS: The Genetics behind the Superheroes of Modern Criminal Investigations

by PAOLO MIGUEL ANICO (Crypton)

Superheroes, as we are familiar with in one form or another, have been used in stories for as long as people remember. From the tales and legends of heroes in our history to the contemporary Pop Culture, there is no shortage of superheroes, or “Supers,” as the film “The Incredibles” calls their specific group of enhanced humans. Supers, as we all know, are fictitious. But contrary to this belief, Supers may actually exist within our communities already.

In various corners of the world, there are a number of people, known as “Superrecognizers,” or SRs, who are able to remember and identify any face that they see. Even ifv they saw someone’s face when they were a child, or saw someone’s face once a decade ago at a concert, they would still be able to recognize these people when they see them again. In this case, some SRs tend to ignore these familiar faces, because they would be accused of stalking. Such an amazing talent is especially useful in jobs like law enforcement, since they would need to single out a possible suspect out of thousands of faces that they see every day. The technological counterpart of super-recognition would be facial recognition, a tool used in many fields to determine the identity of a person using their face. In the same field of law enforcement, facial recognition is a highly popular tool used in investigations. Some governments would prefer to use one over the other—but research suggests that using both in tandem is much more effective. Facial recognition may have its own lapses, even to a point where SRs are more efficient than them, as suggested by Cimmons (2021) in her article in The Washington Post. Based on an example mentioned in the article, facial recognition identified only one in hundreds of rioters, which an SR already recognized. Meanwhile, the SR recognized among the hundreds of other

© Shutterstock

faces involved in a riot. With the use of both, it would have a significant impact in law enforcement, since both use different methodologies in their jobs.

With the emergence of SRs, researchers would have a hard time validating those who are truly SRs from those who only claim to be, since there is little standardized framework established in the academe.

In the effort of mitigating this problem, Ramon (2021) proposed a framework to determine SRs in society. In his efforts, one claim that is misinformed is the saying that “1-2% of the population are super-recognizers” since no diagnostic measures or accepted criteria exist yet, such claims cannot be concluded. A test included in the framework he proposed, also used in the study of Wilmer et. al, (2009), is the Cambridge Face Memory Test (CMFT). Another popular test used in SR determination, or

the diagnosis of developmental prosopagnosia (difficulty recognizing faces - opposite of super-recognition) is the Before They Were Famous (BTWF) test, used in the study of Russell et. al, (2009). This test uses photos of famous celebrities before they became famous such as their childhood photos.

In the study of Russell et. al, (2009), one conclusion is that super-recognition falls at the higher end of the range of face recognition and face perception ability, with the lower tail of the distribution representing those diagnosed with developmental prosopagnosia. Thus, the ability (or disability, in some cases) may be caused by genes influencing the brain’s facespecific mechanisms (in the context of facial recognition), as suggested in the study of Wilmer et. al, (2009). The latters’ research is a twin study, ... continued on next page

wherein two types of twins (monozygotic, or twins from a single zygote, and dizygotic, or twins from two separate zygotes) were utilized. In terms of face-recognition ability, monozygotic twins had a significantly higher correlation score than dizygotic twins, which suggested the high genetic contribution of genes

When

influencing face-specific mechanisms in the brain. Another basis for this conclusion are the studies by Duchaine, et al. (2006), and Woolley, et al. (2008) that showed the heritability of prosopagnosia, “which demonstrated that specific face recognition deficits can run in families.” (Wilmer et al., 2010).

With the emergence of SRs, a standardized framework for the determination of their extraordinary ability is needed so that more studies about them could continue.

Think you are a SuperRecognizer?

Find out by trying out the test at https://www. superrecognisers.com/.

Don’t Match: The Genetics in “Forensic”

DNA Profiles

by KYLE ANIKEHN FRANCISCO (Polyplex)

Themovie Forensic (2020) started with a flashback in a small village where a young boy first sparked his interest in chickens being butchered. Later on he inconspicuously began collecting dismembered animal parts, hiding them under his bed where only he could enjoy them. After the hobby was discovered by his father, the boy was mistreated, abused, and discriminated against because of it. Nothing changed year after year, the boy held on mustering his rage against his father. Later on, the boy had enough and he successfully plotted his father’s murder. No one knew who he was, no one knew what he did. Years later the film progresses with a series of child murders, all of which are blamed upon a boy named Reuben who was mentally ill. Assigned to this case’s forensics team was the medico-legal expert Dr. Samuel. In order to unravel the child murderer’s history Dr. Samuel and the lead detective Ms. Xavier interviewed Reuben’s psychiatrist Dr. Alphonse. After this a profile of Reuben was made and the chase began. The forensics team started analyzing samples found on the sites where the kidnapping took

place. They first started to cross check the DNA samples found on the scene to probable suspects, however none of the DNA matched. Eventually they deduced that the current murders were linked to a serial killer responsible for a series

of murders in the past. The problem was the serial killer in question was apprehended years ago and made out to be innocent. Once the forensics team realized this they realized that the case was deeper than ...continued

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When DNA Profiles Don’t Match: The Genetics in “Forensic”

it seemed. After a while, the police force caught Reuben and later on closed the case without confirming that it was definitely Reuben who murdered the children. The turning point for the film was when the protagonist (Samuel), the head of the forensics team for the case was kidnapped by the real murderer’s henchman. He was able to escape and gather evidence, however he was framed for the kidnapping of another child. After this they had more discoveries which were deeply tied to the past of his brother’s immediate family. Samuel’s niece who they thought was dead, was actually alive and in the custody of the murderer. At this point Samuel already inferred the identity of the real murderer. It was Dr. Alphonse all along. The team assigned to the case was finally able to debunk the elaborate plot concerning the series of murders. Case closed. As a biology student I was intrigued by the laboratory techniques they employed in the movie. For example, the collection of DNA samples were realistic, however I observed the lack of face masks during the collection of the DNA sample from the foil wrapper. The machine utilized for collecting epithelial cells from the wrapper exhibited the vacuum collection method, which is a legitimate process used in obtaining samples. The only downside from that was that it was unclear whether the foil wrapper got rid of other contaminants. It is hard to ensure the non-contamination of DNA on the wrapper when hygienic protocols are not followed. Contamination may be evident when an individual without a face mask speaks near the sample. Aside from this, numerous equipment were used which were normally used for DNA collection, sampling, and analysis such as the centrifuge, and what seemed like a PCR machine.

In order to pinpoint the primary culprit, the forensics team used DNA profiling from epithelial cells and blood samples. At first I thought they matched fingerprints with blood samples. However, as I was reviewing the movie it became clear to me that they matched DNA from the nuclei of epithelial cells. They also collected blood samples from

possible suspects. This is still conflicting for me since DNA matching using blood samples would be exceedingly tedious as compared to using epithelial cells. Blood contains DNA, which is found in the nuclei of the white blood cells, which are not as many in comparison to erythrocytes (Dean, 2005). Meaning they had to pinpoint the white blood cells and harvest them for DNA isolation. They should have just stuck with epithelial cells since all cells in the epithelium contain DNA.

Another conflict for me was the secretive collection of DNA samples which neglected the necessary legal processes. Regardless of the result, I am firm in my belief that they should have followed standard DNA collection protocols. Their dilemma here would be the culprit having a chance to strategize faking his DNA.

They already had the culprit DNA tested, which of course at that time they did not know. However, the DNA of the culprit did not match his own DNA on the wrapper. This is an effect of the bone marrow transplant of the culprit when he had leukemia. Bone marrow transplant also known as hematopoietic stem cell transplantation alters the DNA of the recipient causing DNA chimerism, this chimerism is present in blood and majority of the epithelial cells. However, the cells coming from the fingertips of the recipient still contain some cells with their non-chimeric DNA ( Alsaleh et. al, 2021).

DNA chimerism is the alteration of the DNA in a cell wherein additional nucleotides are added resulting in a recombinant DNA. For Dr. Alphonse’s instance, the DNA in his blood leukocytes contain chimeric DNA from his stem cell transplant, while some of the epithelial cells on his fingertips contained nonchimeric DNA or his original DNA before the transplant.

I would say that this movie gave me a great time, most especially when it was explained why the culprit’s DNA did not match. I may not be a fan of the exaggerated fighting scenes but as a biology major, this was an interesting film for me because of how DNA forensic techniques and loop holes were embedded in the plot. Likewise, it did not conform to the usual hero and anti-hero movies where the antagonist’s plans are easy to discover. Overall, I enjoyed the film because of the battle of wits between Dr. Alphonse and Samuel.

Batch Informosomes: Dynamic Trio Joins the Gene Pool

by KEZIAH FABRICANTE, JAN DEQUITO, AND LOU EBARLE (Informosomes)

are post-ribosomal ribonucleoproteins (mRNPs) that consist of messenger ribonucleic acids (mRNAs) and proteins without ribosomes and ribosomal subunits. These mRNPs are collectively known as informosomes because its RNA component contains information not limited to instructions for protein synthesis while the protein components serve to transfer mRNA from the nucleus to the cytoplasm, to protect mRNA from destruction, and to regulate the rate of protein synthesis.

Informosomes

As the UPLB Genetics Society finally opened the door for brilliant minds to join the gene pool, three outstanding BS Biology students took it upon themselves to accept the challenge of the application process to thrive and become resident members of the organization. Like these mRNPs, Batch Informosomes also have different specialized roles in the organization- to assist, to protect, and to regulate.

Lou Ebarle BS Biology Batch 2021

Lou is the type of friend one would always go to when in need ofa laugh.Their sparkling eyes never fail to brighten anyone’s day whether it is a normal school day or a typical hell weekday in UPLB. One would always spot Lou at Elbi Commons doing schoolwork because not only are they a superb KTV singer, but they are also very diligent with academics. As an escape from the never-ending demands of school, Lou likes to pass time by playing badminton and watching series that make one go hopeless romantic.

Jan Dequito BS Biology Batch 2021

Like a delicate flower, Jan is very gentle and kind. She would always make sure no one feels left out. She is the type of friend who offers her ears and can chat with anyone all day long! She is like a gentle reminder that is needed by everyone, as she will prompt you to take a breath in between those heavy workloads. A fun fact about Jan is that she will go home early after spending time with friends just to stream Taylor Swift. Reading

and watching fantasy are Jan’s go-to pass time. Her all time favorite anime is Hunter x Hunter. For someone who has a brilliant mind, Jan aims to be a researcher after she graduates.

Keziah Fabricante BS Biology Batch 2021

With her courage to accept the challenge as the leader of the pack, KZ never failed to face every battle equipped. Even on difficult days, everyone felt at peace thanks to her comforting smile and uplifting words of wisdom. She is a

woman with beauty and intelligence that make her standout in everything she does. Aside from that, she is the batch’s social butterfly, who enjoys traveling and exploring the beauty of life. Her radiating charm comes with a warm and gentle aura that uplifts the mood of everyone around her. She is also admirable for her wit, courage, and willingness to lend a helping hand. Despite being jam-packed with academic requirements, she allots time to bond with her loved ones, friends, and furbabies. KZ aspires to be a doctor wholeheartedly serving the people.

Informosomes (from left to right) Keziah Fabricante, Lou Ebarle, Jan Dequito

Pandora’s Box: Artificial Intelligence in Forensic Science

Artificialintelligence (AI) has been incorporated in forensic science to identify criminal actions via video analysis, DNA analysis, gunshot detection, and even crime forecasting (Rigano, 2018). Recently, there has been a lot of discourse about the use of artificial intelligence in forensic science, mainly due to a distrust in AI-based digital forensics (Solanke, 2022). These are due to reasonable concerns about the safety of data in digital forensics that may be affected by malware and/or viruses. On top of that, a problem in the justice system could arise from machinegenerated conclusions by misreading patterns in human activity that could lead to incorrect or incomplete inferences. Due to this, the credibility of integrating AI in Forensic Science is questioned. However, we could argue that the benefits outweigh the risks that present itself in using AI. Recent advancements in technology prove that using AI in forensic cases are truly beneficial. One example could be that AI could easily interpret patterns across billions of data and could be used to detect and even prevent crimes such as

by AGNES GUTIERREZ (Allosyndesis)

transportation of illegal goods, terrorist activities, and human trafficking with the help of a public-private partnerships (Quest et al., 2018). AI has also been used in fraud detection like in the company Paypal, which continuously improved their fraud detection AI algorithms by recognizing anomalous patterns and learning to recognize new patterns (Rigano, 2018). Algorithms via AI are currently aiding prominent fields of Forensic Science by leading in data analysis, pattern recognition, image processing, computer vision, data mining, graphical modelling, among others (Jadhav et al. 2020).

We could all agree that technology such as AI is not perfect. Hence, there could be some loopholes present. There were some cases wherein banks had false suspicious activity alerts due to unknown events where the AI model has not been trained. In one situation, a bank has mitigated the internal risk by designing a more transparent machine-learning model. Another risk of using AI is that cybercriminals might obtain an “information advantage” via malware and viruses. As technology improves

capacities, so does AI increase its dangers. According to the CTO for Recorded Future, Stefan Truvé, “Criminals and rogue states are building autonomous weapons and won’t be following any international conventions.” A solution to this is to increase and develop cybersecurity defense strategy (Johnson, 2019). As such, recalibration is also needed for more complex cases. With these things being said, it makes us think that the potential of AI is not only limited to its advantages, but to its disadvantages as well. Is AI just like Pandora’s box with its evil awaiting to be unleashed? Indeed, there is an ongoing battle in fighting the dangers of using AI, but we also have a good counterattack: by using AI. By being aware of the risks of AI, we can adapt our response and solution towards improving AI. In leveraging the best practices starting from training data, to scanning, to hardening the model and data from any distortion, and lastly recalibrating, it can be believed that good AI could fight the bad AI to keep the Pandora’s box from opening. In turn, this may lead towards the promising future of AI and forensic science.

Lurking Problems

by KOOZAE CALVIN UMALI (Hachimoji)

Last October 11, 2022, the Philippine House of Representatives, through its committee on Public Order and Safety, approved the consolidation of the proposed bills that would create the Philippine DNA database system. In a utopian world, a Philippine DNA database system could be a blessing; but in the current state of the nation, it could be a disaster.

DNA databases are banks of genetic profiles which can be used from the field of medicine to genealogy, and often and most heard of, in forensics for criminal investigations. Given the overwhelming similarity of the human genome across all individuals, DNA databases use short-tandem repeats, which are repeating units from non-protein coding regions of the DNA, that are easy to compare among individuals.

The first DNA database was created in United Kingdom in 1995. Since then, other nations have followed suit and created their own national DNA databases. The Philippines, when compared to some of its ASEAN counterparts, does not have a national database.

House Bills (HB) 94 and 540 wants to establish a Philippine National Forensic Database. The

former will include DNA from crime scenes, arrested, detained, and convicted individuals, uniformed and armed personnel, missing persons, and voluntary persons, while the latter will also include DNA from street children, beggars, and unidentified human remains.

In the context of DNA used in criminal investigation, the Philippine Supreme Court in 2007 recognized DNA as admissible evidence in trials and court proceedings, and through its “Rule on DNA evidence” laid out the procedures for the conduct of DNA testing and guidelines on how it can be applied to cases.

But even though the rule has been on land and in effect for eight years, the problems facing our forensic and criminal agencies in DNA testing would show that creating our own DNA database could be far from happening.

The biggest roadblock would be in the budget allocation. In the paper of Rodriguez et al. (2020), they cited the inadequate government support for the expensive DNA testing, which makes the collection of samples highly selective. If there are backlogs from DNA testing due to lack of funds, how more can we create and sustain a database of samples?

Moreover, the budget for the equipment and facilities where these will be created and will be running should also be financially supported by the government. More DNA laboratories should have been set up across the country before putting up a database system. Only three DNA laboratories are used for criminal investigation: one in NBI under DOJ, PNP under DOJ, and the DAL in NSRI under UP.

Ethical issues can also be raised, especially with the clause including DNA samples from street children and beggars. It raises the question, why them? Is this a prejudice that relates crimes to their socio-economic status? Is the Philippine National Police credible enough to handle the database, as suggested in the bill? Recall that recently, some members of the PNP have been found guilty of planting evidences to some innocent individuals in the brutal Oplan Tokhang.

During the public hearing of the said bills, Dr, Eva Maria Cutiongco dela Paz, the Executive Director of the National Institutes of Health, said that the NIH and UP-PGH support the creation of the said database for forensic use only. But how are we sure that the individuals with access to the database will only use it

for gathering evidence for court investigations?

The creation of the Philippine DNA database system will benefit the PH criminal justice system, but the lurking problems of the country, not just with the DNA testing, will overshadow the benefits that the database will provide.

© David Parker | Science Photo Library | Getty Images

20 EDITORIAL Insights from Forensics: Fixing a Broken System

The prevailing death investigation system in the country is said to be the medico-legal death investigation (MLDI) system which combines medical and legal expertise to answer salient questions of a crime scene, including the cause and manner of death, typically that of unnatural or suspicious death. According to the MLDI module developed by Global Health Advocacy Incubator and CDC Foundation, MLDI is “a process whereby a coroner, medical examiner, or forensic pathologist working with the police, seeks to understand how and why a person died.” Its purpose is to provide medical findings and analysis that may be submitted as evidence in court.

Surprisingly, we have no particular Law for MLDI. The Sanitation Code served as the only relevant part of our death investigation system discussing the proper disposal of bodies, exhumation of remains, etc. until 2019 when the House of Representatives approved the House Bill 9072 or the “Mandatory Autopsy Law” which states:

This Act requires mandatory full autopsy and prohibits the unauthorized disposition of human remains arising from deaths under investigation or mysterious and suspicious circumstances.

Moreover, the personnels mandated to perform the autopsy and dissection of remains are: government health officers; medical officers of law enforcement agencies; and members of the medical staff of accredited hospitals.

Despite this Act, medico-legal services remain inaccessible to most citizens because of few facilities and experts in the field. These services are bound to regional offices and there is no systematic transportation scheme for death investigators to go to remote areas or for the body to be properly brought back for examination. Another limitation is that we lack forensic pathologiststhe medical experts best suited for death investigations.

According to the MLDI module, the forensic pathologist “acts as the case coordinator for the medical and forensic scientific assessment of a given death, making sure that the appropriate procedures and evidence collection techniques are applied to the body.” Forensic pathologists are specially trained to conduct forensic autopsy, to obtain medical evidence in the crime scene, and to form accurate medical findings.

Unfortunately, there are only two forensic pathologists in the country, Dr. Cecilia Lim and Dr. Raquel Fortun. The road to becoming a forensic pathologist is quite long and difficult, and often the expenses are high. One must earn a bachelor’s degree, then a medical degree, and extensive years of education and training in anatomic, clinical and/ or forensic pathology followed by

a one-year residency in forensic pathology. There are a few universities in the Philippines that offer the undergraduate degree program BS Forensic Science such as De La Salle University (DLSU) and Lyceum of the Philippines (LPU). However the post-graduate medical training in forensic pathology is only available abroad. Most of our Filipino forensic pathologists are actually practicing their profession in other countries.

Without a Law that requires forensic pathologists in our death investigation system, they have no employment opportunities here.

One of the most revolutionary discoveries in forensic science is DNA fingerprinting or DNA profiling. It is a laboratory technique for human identification based on the variation in nucleotide sequences of specific regions of the DNA that vary among individuals. Currently, there are only three government institutions that conduct DNA tests for criminal investigations: the Philippine National Police (PNP), the National Bureau of Investigation (NBI), and the University of the Philippines through the DNA Analysis Laboratory (UP-DAL). Rodriguez et al. (2021) also pointed out the high cost of DNA testing due to insufficient government support and the absence of a national system for the routine collection and processing of samples and analysis of evidence. This means we are still far behind the full utilization of forensic DNA technology in the country.

The undervalued field of forensic science in the Philippines is taking a toll on our justice system. Over the years, we have heard of controversial criminal cases wherein medico-legal reports contain incomplete information, evidences were mishandled or neglectfully destroyed, and conclusions were prematurely formed based on a few evidence. One example is the case of Christine Dacera who was found unconscious at a hotel bathtub during New Year’s day. The police hastily declared that it was a rape-slay case despite insufficient evidence. It was also revealed that Christine’s body

by IVIEN FETALINO (Reprimo)

was embalmed prior to medico-legal examination thus contaminating any viable sample for DNA analysis, toxicology tests, and histopathology examination. After the second autopsy by the NBI, it was concluded that Christine died from aortic aneurysm which was considered to be a medical condition not a result of rape or drug intoxication. Christine’s case is just one of the few major headlines that exposed the broken system of the Philippine death investigation while many deaths, unnoticed by the public, were possibly left unsolved.

In our own judicial system, testimonial evidence is valued more than other types of evidence; this is sometimes unreliable due to the subjective nature of testimonials and the limitations of the human memory especially with the passage of time.

Based on a study by Strange and Takarangi (2015), traumatic events could leave distorted memories in which mental imagery has an important role to play. Hence, forensic science provides an objective means to discern the truth when testimonial evidence is questionable. Autopsy results and DNA profiles are valuable evidence that should complement testimonial evidence, and by itself, should be considered strong evidence in court.

Forensic science, with its multidisciplinary approach involving forensic laboratory disciplines, forensic pathology, forensic entomology, and recently emerging digital forensics, is a crucial element of the criminal justice system. It could fill gaps in crime investigations and could shed light to unresolved crimes. By enforcing science-based policies and standardized protocols in crime scene investigations equipped with transparency and accountability of the authorities and institutions involved, we can mend the faulty system of criminal investigation in the Philippines and defend truth and justice for every Filipino.